--buildpkgonly doesn't work for any packages whose dependencies aren't already fully satisfied, including being up-to-date.
You simply cannot use --buildpkgonly for a world update save for the very trivial transactions, for which any of what I mentioned isn't a problem anyway.
I did not realize you were a Gentoo contributor when I first responded!
This is an interesting problem for sure. I don't know enough about portage internals to know whether it could be fixed easily, but it would be very nice to have.
So far I haven't really ran into any consistency issues caused by non-atomic upgrades. The only thing that comes to mind is needing to restart a zsh instance that was running during an upgrade that included it, and Firefox will sometimes tell me it needs to restart!
I have a fairly fast CPU (ryzen 3900x) so the time spent in an inconsistent state is probably much shorter than it is for others, I suppose this is why it's never bothered me before.
