Is the museum+ version allowed? If so, which console does it go under? I don't own museum+ yet but I do plan to.

its allowed,you can put it under arcade or switch

The Muesum+ version is allowed, yes. All the consoles it was released on are available as options when submitting a run - if you click the little "+" next to the consoles at the top of the page, you can see all of them there. The GBA version is preferred due to being more thoroughly explored, but Museum+ is perfectly fine to run on. Good luck!