Recursive chmod (or chown) has been breaking things since before systemd was a thing, so even if systemd is now responsible for stopping things from working, it can’t have been that previously, especially at the time I might have done something silly.

As for repairing permissions only, I suppose it would be possible, assuming the system still works (or can somehow be encouraged to do so) to copy only the permissions (or at least infer them) from a backup or something rather than the whole files.