It would be just a package exactly like any other. Already, if I am not mistaken, if you put a module of the same name in sites/all/modules then it will win over the core modules. If that's not so anymore, it'll be too easy to change.
Regards NK ---------------- I believe this is true as I just did it on a Acquia site that had some of their package in a subdirectory of /modules (non-core contrib). However I wound up with conflicts somewhere as some parts of the theme no longer worked. I fixed it by downloading all the Acquia approved modules to /sites/all/modules and deleting the Acquia versions. I have no idea if theirs were vanilla off contrib or if they had tweeked them. I did not do a careful experiment to find out exactly what caused the problem (problem was the theme config page did not save its results to the database so it had no effect). I think what Acquia is doing is a precursor of some of the discussion here. So this is a warning that there be dragons there.