IMHO the loyalty traits display how loyal you are, not how loyal you are to something. So if you've sworn to the Emperor and the Order it would be very hard for you to break that oath, unless you were loyal to something else (i.e. Fritz in KotR being loyal to the Illuminati) over the top of that.
Vissa, for a counter example, is not loyal at all and may actually rebel at the drop of a hat. I hadn't even noticed, since he was piling up absurd traits from the supply system anyway. As long as the game doesn't decide to rebel him it'll make for a fun ride.
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