Is it allowed to submit the same run for multiple categories? I noticed, for example, that I think my run under the All Bosses category would be valid for the No Major Glitches category as well. Can I submit my All Bosses run under the No Major Glitches category?

Yeah, you can, but only if you don't use any major glitches.

Si es aceptable, he visto varios jugadores que suelen enviar no sólo en AB, sino que en otras categorías tambien. Siempre y cuando las reglas de las categorías se adapten a tu speedrun.

A good rule of thumb is that all valid NMG runs are valid 1.1+ runs. But not all valid 1.1+ runs are valid NMG runs. So running on 1.2, avoiding beppi skip and avoiding Luigi Swaps pretty much keeps it valid for both categories for the most part.