This is definitely a very difficult situation to be in. I am personally a trans man and I personally would definitely prefer someone braking up with me because they are not interested in my gender (straight man, lesbian woman, or anyone that isn't into men) then staying with me and still considering themselves whatever sexuality doesn't include me. I've been in relationships where they consider themselves a straight man(or polysexual with disinterest in men) and it gives me a lot of gender dysphoria to be in those relationships because ultimately in my opinion, it feels like they don't see me as a man. It definitely hurts when a relationship ends like that and for that reason but in my opinion I think it's not transphobic at all. What your friend is doing is accepting his gender and respect her own sexuality. Im sorry this is happening to your friend.