Tested what you say, but still the same problem.
It seems that `git bz apply` does make a git am -iu3:
/usr/local/bin/git-bz (line 1498):
process = git.am(filename, **{'_interactive':True, '3':True})
If sometimes this trick works for you, maybe you don't have the last version of
git-bz
(http://wiki.koha-community.org/wiki/Git_bz_configuration#testing_with_-3_flag_set)