Ah, that could be it, my Unity 2020.3 was already 2020.3.11, so maybe they changed something about it...
As for that message, it's not exactly saying there are some files missing (and they're definitely in my checkout), but something else is weird about them. Maybe it thinks they should be links to somewhere and for some reason the real files are there?
I haven't seen a message like that until now, and I'm using git for quite a while and quite a lot at work...