> Since many use cases for /etc/systemd unit files just include the respective /lib/systemd file and add a dependency or similar simple extensions, that won't work.
Why not? You'd still get the warning that /lib/systemd/foo was newer than /etc/systemd/foo. And that would let you know to double-check that things are still OK, and to touch /etc/systemd/foo when you're satisfied.
The case where a timestamp check _would_ fail is if the /lib files retain their upstream timestamps rather than the installation timestamps -- then upgrading systemd might install a "new to you" config file that's still older than the last time you touched the corresponding file in /etc.