This bit:

cd ${test_tmpdir}
rm -rf test2-checkout
$OSTREE checkout test2 test2-checkout
stat '--format=%Y' test2-checkout/baz/cow > cow-mtime
assert_file_has_content cow-mtime 0
echo "ok content mtime"


is asserting that the checked out file has mtime 0 (because it's a hardlink into the repo).  But for bare-user, we need checkout -U for that.