I'm a bit surprised by this. Whenever I update a core module (which, admittingly, I don't do very often), it always install itself in lib/VERSION, not in site_lib.

If it didn't, you wouldn't be able to "seamlessly" upgrade CPAN (the CPAN shell always checks to see if there's a newer version available).

So, I don't have an answer. I always assumed it would just work (and it always has for me).