Windows Update only very rarely changes startup entries.
And there would be a very simple way to allow Windows "native tasks"... if Microsoft would follow their own recommendations.
For software that wants the "Certified for Vista" logo, each executable of that software needs to be codesigned. When software is codesigned, it can be verified that it comes from a specific source. Well, guess what - Microsoft doesn't even codesign their own Vista files. If they would, things would be a lot easier!