Right, in the end OverPy optimizes the gamemodes… which includes the removal of unused code ^^
You can manually uncomment the rules and add the @Disabled annotation instead, but I understand this is annoying if you still wish to program in the UI.
For the 0 -> False/Null replacements, rest assured I have tested every single one of these to make sure they behave correctly. However I agree that this leads to reading confusion if you program in the UI, in an upcoming update they will only be applied with the #!optimizeForSize compiler option.