As far as I know the 4 passives are tied to the specific ship - and each T5U/T6 ship has a different sent of passives. The Master Trait can be transferred directly to the character once he has unlocked it on the ship. Once you transfer the Master Trait it is yours forever, no matter what ship you use.
STO is about my Liberated Borg Federation Captain with his Breen 1st Officer, Jem'Hadar Tactical Officer, Liberated Borg Engineering Officer, Android Ops Officer, Photonic Science Officer, Gorn Science Officer, and Reman Medical Officer jumping into their Jem'Hadar Carrier and flying off to do missions for the new Romulan Empire. But for some players allowing a T5 Connie to be used breaks the canon in the game.
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