But isn’t the point of a source only distribution like Gentoo, to build everything yourself? Who is running gentoo but also lugging around old precompiled stuff they don’t have the source for?

As the post describes, the problem is that on Gentoo you can’t really build everything then switch binaries for everything, or at least that’s not what happens when you update things the usual way.

Instead, dependencies are built and then installed, then dependents are built against the installed versions and then installed, etc. In the middle of this process, the system can technically be half-broken, because it could be attempting to run older dependents against newer dependencies. Usually this is not a real problem. Because of how pervasive time_t is, though, the half-broken state here is potentially very broken to the point that you may be unable to resume the update process if anything breaks for any reason.