I didn; t notice this before, but the hover effect for the tabs seems to be working now. They're still not positioned correctly though, and the size is still very different compared to other vaultwiki installs.
EDIT: I've done some more testing, and as far as I can tell the function special_query_templates in vault/special_admin_template.php isn't ran at all when rebuilding styles. I've added a line to send a mail to myself inside the function, but it simply never gets to that point.
EDIT2: nevermind, I got it to work now. The fix you provided does work as long as I use the correct tool to rebuild the styles (apparently rebuilding from the update counters page does not do the trick, rebuilding using your link does).
Just one small issue remains, a margin causes some space between the bottom of the tabs and the top of the article. But I can easily correct this myself.
.p-cactions { margin: 0; }