My game doesn't work properly, so I can't play. Should I use community fixes? It is allowed? (for any%)

Unfortunately Sneaky Upgrade gives some small advantages over playing vanilla even without adjusting any settings (like remembering your difficulty setting between missions), so it's not really allowed. What I mean with "not really" is that there hasn't been a solid decision made by the community yet since the game hasn't been very active.

Another reason for using the vanilla version is the load remover. Because of the massive load times it is required to submit load remover timing and it doesn't work with Sneaky from what I've tested it.

IL runs and Gold Mod runs allow the use of Sneaky. We could start a discussion about Sneaky in the Thief speedrunning Discord, and maybe add it as a modifier. That would still not solve the load remover issue.

Bit late to reply, but the GOG version runs mostly without issues.

So if SU is a no-no, that would be the alternative.