Is the Neonix Patch allowed? or do I need to use the Vanilla version of the game?

As long as the changes are just visual and not changing anything physically (physics/object location/player movement/enemy movements/gates or walls obstructions) in the game that doesnt leads to an advantage playing on it, it should be fine. Though you may be asked to reupload the run on original version if the run on modded version cannot be verified for some related reason.