There was one more test suite failure when run on FAT, which I've investigated today. It turns out that a bug report was filed about the same problem, and at root it seems to be a bug in git merge. Luckily, it was not hard to work around the strange merge behavior.
It's been very worthwhile running the test suite on FAT; it's pointed me at several problems with adjusted branches over the past weeks. It would be good to add another test suite pass to test adjusted branches explicitly, but when I tried adding that, there were a lot of failures where the test suite is confused by adjusted branch behavior and would need to be taught about it.
I've released git-annex 6.20160613. If you're using v6 repositories and especially adjusted branches, you should upgrade since it has many fixes.