Well, I checked and it looks like none of my .git repos are backed up. All attempts to restore only restore the working copy. -_- I'm not sure why it was working for the person in the comment I linked.
Update: Deleting C:\Programdata\Backblaze\bzdata\bzexcluderules_mandatory.xml resolved the problem for me. Seems like at one point[1] they started excluding .git directories by default, got a bunch of backlash, reverted that change, but never changed the setting back for some users (like me).
That's a really important fact that's getting buried so I'd like to highlight it here.