are you allowed to use auto keyboard (https://www.murgee.com/auto-keyboard/) for the fast weapon switch glitch in a run? can you even do the glitch without it?

Nope, that's a macros and it's not allowed. Learning how to mash can take some time but it's definitely more doable in this game. To get optimal damage output you only have to mash between 7 and 8 times per second on ground stages. Mashing any faster will result in damage loss.