The missing council cutscene suggests that you may have hit another bug, entirely not related with the sex reassignment you've attempted. If you fought the handmaidens *after* you spoke to Atris, your companions were forcibly removed from the party and placed next to the training mat to act as bystanders. After the fight they'll just sit there and you can't interact with them. I'm not aware of any solution to this problem, short of reloading an earlier save. I've experienced this both in vanilla and with TSLRCM 1.7 installed. So, make sure you have your companions with you when you board the Ebon Hawk and correct the above glitch if necessary.
Hope this helps.