I want to get back into speedrunning and in particular this game. I used to run AM2R a lot, the only problem is that I have gotten used to the morph ball button (a seperate button that you have to press only once to morph). Is it allowed to program my controller in a way so that I can only press 1 button to morph?

Since that isn't something you can do on the original hardware, I don't think that would be allowed as it would provide a significant advantage over the original hardware. It wouldn't work the same as in AM2R anyway, it would be very janky due to the way morphing works in this game.

Yeah, I guess that would be true. Guess i need to get used to it again, it will probably be a matter of minutes anyways lol.

This would definitely be against the rules. Allowing something like this would open a huge can of worms.

What about multi-binding down buttons? Giving a down direction for each hand would allow for faster morph ball with the use of timing 2 separate fingers.

Multibinding isn't a feature on the original gba but Multibinding is a feature on the wiiU VC that cannot be turned off. in theory multiple gamecube controllers can mimic Multibinding on the gameboy player.

It's not really an original console vs. emulator discussion. The WiiU VC has savestates which are banned for example, and similarly I could create a controller that has a button macro which would also be banned. Binding down to two different buttons seems fine to me though even if it doesn't work as well as you described on the gameboy player. If I press down on my gamecube controller and then on my SP for example it only registers one down input.