Seeing as all disguises stay level 1 for the entire duration of an Any% run, I don't think it makes sense that you should be allowed to level up the disguises by replaying a level.

Glad to see you doing ILs though! Hope you keep doing them!

The rules state:

"All runs must be done from blank save files on official releases."

Since TM++ is not an official release, it is not allowed for runs. Emulators are specifically adressed in the rules and are therefore allowed for runs.

The IL rules state:

"Play a level as you would in an Any% run, which means that all treasures for the episode are unopened to start. Timing for this category goes by the in game timer displayed after the episode."

So you may only upgrade the disguises to the level they would reach in the Any% route for that specific episode.