If you've installed lots of overlays, you'll notice that on upgrading, certain packages that are in the overlay are pulled. There should be an option to not allow that to happen unless you strictly specify the version. A possible value in FEATURE? Reproducible: Always Steps to Reproduce:
In portage-2.2 you can use atom::repo in package.mask (part of bug 185377), in order to mask versions from a specific repo (also involves bug 262038). Maybe this helps you accomplish your goal?
That looks good. Close this one?
I guess we can consider this as a duplicate of bug 185377. *** This bug has been marked as a duplicate of bug 185377 ***