If you look at this line of code:
https://github.com/yoshinorim/mha4mysql-manager/blob/master/lib/MHA/MasterMonito
r.pm#L415
It looks to me that masterha_check_repl skips all slave checks when using MySQL
5.6 with GTIDS enabled.
Some of the slave checks are valid even when using GTIDs. For example, it
doesn't verify that the MySQL user specified in the MHA configuration can
connect to the master and has replication client privileges.
I can gather more information, if necessary.