Map of necessary map squares
Map of all necessary map-squares (for NTSC and PAL together): (last update: 04.10.2017; Moonfall application allows to skip some more map tiles, and a SuperJump in Tourian escape was confirmed by Sniq being possible with R-Tank and a space pirate through a ceiling)
This section here is so far completely solved, except of one potentially not necessary square in Tourian, and some potential SuperJumps to reduce the number of visits of squares as explained below.
Current map: https://i.imgur.com/9j1vKg0.png
(Old, outdated map: https://i.imgur.com/o9MVfgt.png)
Procedure:
For every single square within the map, it has been checked if there exists a route/playthrough (without OoB or SpaceTime-Beam) of Super Metroid that does not activate (i.e. colour a square pink) that given map-square. If such a route does not exist (i.e. the square is within the intersection of all existing routes), the square is called "necessary".
For all squares that are not blue, there already has been found a method to avoid those squares [and two cases were distinguished where the method to avoid such a square was either obvious (= green) or not obvious (= red)]. The bright-blue squares are squares that get automatically filled into the map (after defeating Kraid, Draygon or Lower-Norfair-Ridley), but in principle one would not have to go there.
[For Ceres Ridley´s square, the square will not get filled if one does not go back to that room after the fight.]
Note that the only other Map-Square, that might otherwise not be necessary, is the one to the left of the blue square at the door to the right in the last Tourian escape room in Tourian, but this could if at all only be skipped if one could further below in this room (using space pirates or their projectiles) execute a X-Mode setup on one of the small platforms for a SuperJump (with beforehand prepared FlashSuit) through the long platform next to the door.
Number of necessary map-squares per area, and total number of necessary map-squares:
Ceres: 11.
Crateria: 52.
Brinstar: 35 + 3 automatically added squares in Kraids room.
Wrecked Ship: 8.
Norfair: 29 + 1 automatically added square in Ridleys room.
Maridia: 13 + 3 automatically added squares in Draygons room.
Tourian: 59.
Altogether: 207 + 7 = 214 automatically added squares.
Another map that also shows how often the necessary squares have to be activated:
Current map: https://i.imgur.com/BDyiUKV.png
(Old, outdated map: http://i.imgur.com/NR0kxLN.png)
Blue squares: Only needs to be visited once.
Violet squares: Only needs to be visited twice.
Black squares: Only needs to be visited three times.
Golden square (at parlor room): Only needs to be visited four times.
The squares above the ship do not need to be activated twice, since in the Tourian escape, the map stops working as soon as Samus enters the ship (which one can observe in the Mini-Map), but in theory, the ship moves back through those squares.
Note that in the Colosseum, it might be possible for TAS to get R-Mode in there, then freeze a mocktroid beneath the left coloumn for a Springball-jump with reserves kicking in and then Freeze-Climbing using Grapple to be able to use X-Ray and pushing Samus through the inner non-solid part to the right side to skip entering the 4th upper blue square on top of the room from the right when going towards Draygon (but not when coming back).
On the way back up in Wrecked Ship in the long vertical central shaft room, it might be possible to skip through some Map-Squares via SuperJump setups at slopes further below in the room. The same principle might hold on the way back from Ridley, in the Ridley-PB room, for the square above the sqaure of the left lower door, aswell as in the shaft room above this room, again on the way back. The same principle might hold for the square beneath the square in which the elevator platform in the Norfair room connecting to Brinstar is (but not for other squares in there since entering the outer elevator transition blocks from within the shaft after SuperJumping into there gets Samus back down after exiting that room.
Sidenote:
If one rides the elevator from Brinstar down to Norfair, then the map square directly below the square in which the elevator platform in Brinstar is located at will not be activated. It will be activated when riding up the elevator back to Brinstar from Norfair, though.
Argumentation for why the with red (and green) colour outlined map-squares are not necessary:
[For all the green outlined areas, since corresponding routes can easily be found for individual map-squares that are part of those areas, it is left as an exercise to the reader to find routes for each single map-square of those that do not use that map-square.]
1. The path below the Gauntlet can be skipped entirely by using the Gauntlet if one wants to exit the ship´s area, and by using the way back from WS to the ship area whenever needed.
2. The whole red coloured area between WS and Samus´ ship can also be skipped entirely by going through Maridia suitless and entering WS from the right side and leaving it to the right side, too, since all of the other areas can be done without Gravity aswell. The same still holds also for the area near the early powerbombs in Red Brinstar, since one can collect Crocomire´s powerbombs instead.
3. By using the Big-Metroid-Skip method for example, one does not have to enter the refill-room in Tourian after the big Metroid´s room, and one can skip all of the red coloured squares in the 3rd escape room simultaneously by shinesparking through the floor from below at the end of that room. In the 4th escape room, for each red coloured square, one can easily find a route (that is still fast enough) that does not use that specific square.
4. For the red coloured squares near SporeSpawn, one can either skip all of the area near and behind SporeSpawn completely, or just use exactly this path past SporeSpawn in order to skip the squares within Charge-beam´s room, and one can get back via the elevator in Red Brinstar, too.
5. Although one has to visit Ceres-Ridley´s room (in Ceres), the mini-map will not show that map-square after the fight unless one re-enters that room afterwards.
6. In the room before the so-called "noob-bridge", via appropriate spinjumps or damage-boosts respectively, one can choose if one uses the upper-right or the lower-left square for each of those two pairs of squares, in order to proceed.[Furthermore, it is even possible to travel diagonally through those map-squares in both cases without entering any of those four squares, and the same holds even for the way back (using precise jumps and bombjumps).]
7. The lower part of Red Brinstar and the area on the left side of the breakable glass-tube can be completely skipped by going to WS early, getting Gravity and using the so-called "forgotten highway" to get from WS to Maridia, and then after finishing Norfair, one can get back by going upwards in the glass-tube room. Furthermore, by obtaining Ice in Norfair and doing a GGG that uses the freeze-walk principle, one can even skip the glass-tube´s square:
https://www.youtube.com/watch?v=ZYRCKxfKURg]https://www.youtube.com/watch?v=ZYRCKxfKURg
8. In Kraid´s lair, one does not have to get Varia nor visit the lower red outlined square near the elevator at all, because one can get Gravity instead or do some jumps across that gap in the elevator room respectively, and hence those squares are not necessary.
9. All the red outlined squares in Maridia on the left side of the Colosseum [= pre-pre-Draygon room, filled with mocktroids], can be completely skipped via the Botwoon-skip route with Gravity that uses the Freeze-Walk method in order to get past a grey door:
https://www.youtube.com/watch?v=vOiAzuZBXPE]https://www.youtube.com/watch?v=vOiAzuZBXPE
10. For some of the squares within the Colosseum (the red outlined ones), one can find a simple route for each of those squares that circumvent entering that given square for both ways: Getting to Draygon aswell as getting back. Also, one does not need to collect SpaceJump at all.
11. Existence of the Gravity-Speedbooster category proves that the area around Ice does not have to be entered. The same holds the other way around for Speedbooster area up to pre-Bubble-mountain room (from Speedbooster´s point of view) via the Gravity-Ice category. Also, in both of those categories, one does not have to enter the area around Crocomire up to pre-Bubble-mountain room (this time from Crocomire´s point of view) either.
12. In order to skip the upper Norfair path (leading to Bubble-mountain room) and Bubble-mountain room altogether, one can obtain the Shinespark-Suit at Draygon for example, and use a shinespark to get through the long hall on the right side of the upper Norfair savestation, followed by using the lower route to Lower Norfair and get back afterwards via the green-gate room above and near Crocomire.
13. For the squares in the lavapit room at the entrance to Lower Norfair, one can simply use SpaceJump with Gravity to skip those.
14. By leaving Lower Norfair using the same path that was used to get in there, one can skip the area near its exit aswell as the area around Wave entirely.
15. Skipping the room in Lower Norfair with the breakable columns and the yellow-pirates shaft there can be accomplished by ice-clipping through a platform in Mickey-Mouse room:
https://www.youtube.com/watch?v=vu0Hpxu8Og4]https://www.youtube.com/watch?v=vu0Hpxu8Og4
16. Using SpaceJump, for almost all of the red outlined map-squares within the rising-acid room in Lower Norfair, one can find a route through this room that does not use such a given red outlined square. And for the one square connecting to the necessary square of the door on the right side in this room, which is on its left side, one can use an appropriate shinespark through a 1/2-block thick slope in the ledge near the door in order to skip it:
https://www.youtube.com/watch?v=g21i1Vj3ymQ]https://www.youtube.com/watch?v=g21i1Vj3ymQ
17. Using the recent God-Mode exploit, one can skip all squares starting near lavapit to Lower Norfair up to the huge acid room:
https://www.youtube.com/watch?v=uHxK6J-fQ1M]https://www.youtube.com/watch?v=uHxK6J-fQ1M
18. Moonfall in the Green Brinstar elevator room allows to get powerbombs from the Etecoon area, and then one can go up and around towards Wrecked Ship or down to Red Brinstar, in order to skip some of the western map squares.
19. In the 3rd Tourian escape room, one can use an R-Tank and have a Flashsuit and use a space pirate there to spark through the ceiling to skip 4 map squares there.
Argumentation for the necessity of the blue squares can be done by testing all known mechanics for all areas.
Actually, in order to argue that certain squares are necessary, the only way would be to mention all currently known possible maneuvers that could potentially be applied, and then to explain why they do not suffice to skip the given blue squares. But explanations on why the blue squares need to be activated could be added if it is unclear, but for the most parts, looking into SMILE to see the Scroll Areas should help.