The candle lights in the church SE unmodified don't move at all, the sprites are identical. They only move in the classic version. Most other rooms have proper moving candle lights, but not the church. That's why I want to fix it.
As for the pixels, even though some may not be bothered by them, I fix them because they look crappy and sloppy. Left overs that don't fit the new environment.
And yes you can delete specific room fixes and leave others so you have the fixes to want. Though it might be hard in some cases to know what fixes you want and which you don't, I'll make sure the readme is detailed enough so you can remove any unwanted fixes.