Your Mint/Xed example doesn't show what you think it does. Mint doesn't just ship with .desktop entries for a bunch of applications, they are still managed by the respective developers and part of the packages themselves. Mint is also the developer of Xed, so the repository is in their organization, but the .desktop file is still part of the package. If you install Xed on any other distribution, you'll still get the same .desktop entry, because it's part of the package.
That is all I've been talking about. I'm not sure how your reply relates to that, but it would help me if you tell me what you're arguing against.