Parts Editor
If this isn't the default function it should be a mode you can toggle. The parts editor should do nothing at all to the main score when you change parts. You should be able to remove entire phrases from parts and not have it change a single thing about the score. I would rather make an edit twice (once in part, once in score) then have to change a given thing over 15 times like in the current system.
Comments
Can you explain what you mean in more detail? The whole point of parts is for them to actually reflect what's in the score; it would kind of be a disaster to attempt to publish or perform a piece in which this wasn't the case. What are the circumstances that are causing you to want notes in the p[art that are not in the score? If you really truly want that, you can simply do "save as" in the part, which will create a separate file just for that score, not linked at all. But I'm not understanding what the rationale for this would be.