I would imagine a plug-in would work for some instances, depending on what you wanted to do.
Technically it's branching if you start coding in core files which break compatibility with the source, and given the strong following that wordpress currently has, it might be counter productive to branch to another distribution which would eventually require full time development, or would eventually die out.
So Plug-In is probably best for functionality requirements. Looking around, I have seen people make plug-ins to modify the apperance of the admin areas as well.
I just brought it up, because I do remember doing some work, and the end result was that they would not be able to preserve those development changes without redoing them. But that was way back in version 2 or so...
Sometimes it can be expendable... sometimes you don't want it to be expendable, so... hope that helps.