There are many different control schemes used, even when comparing some of the best Super Metroid players. With that in mind, try to find what's most comfortable for you instead of blindly copying another player's control scheme.
Be aware that if you wish to place Dash on L or R, you cannot reassign the Angle Up or Angle Down buttons (however, if you happen to be playing on Wii U Virtual Console, you can remap buttons appropriately in its menu to compensate). Some schemes may be more conducive to "claw" grips (pulling your index finger above the pad, typically to reach the X and/or Y buttons), and some schemes may be more conducive to "fat finger" grips (using your thumb almost exclusively to control the face buttons). You do not have to limit yourself to a specific method of holding the controller because many times, room transitions will give you plenty of time to change your hand orientation.
Below are control schemes used by many of the best Super Metroid players. The first control scheme is the default control scheme for the game and the rest are variations. For example, the second control scheme is the same, but with item select and item cancel swapped around.
Foosda - Demonstrates how to use the fat finger grip.