I agree that it would make more sense for Any% (does not use cheats) to simply be called Any%, and for Any% (uses cheats) to be called Cheat%, removing the need for the Any% subcategory.

As for cheats being allowed in All Missions, we use the pile increase cheat so we can complete all of the missions as fast as possible without worrying about picking up XS items. In normal Any% you need to route how many XS items you collect in each level, in order to have enough to unlock each subsequent level and eventually reach the final level. The main idea of All Missions is to do all the skips and timesaves you can do, complete each level as fast as possible regardless of how many XS items are skipped in the process, and then use the pile increase cheat to compensate for the missing items to unlock the next level. It's like doing Any% for every IL in one run. But I wouldn't mind a variant of All Missions without cheats being added if people wanted it.