to give a different perspective... I am both trans (maab and living as a girl for 2 yrs now) and BPD and I think my BPD was a big reason I transitioned. I don't think I would have done it without the identity problems i have from BPD (and attachment, cuz of my boyfriend who is the only reason i am still transitioned.) I mean in a lot of ways I don't feel like a boy but I think I was clinging to being trans to fill in for a lack of an identity. But I think I suffer really deeply from the borderline symptoms in terms of functioning, so it might be different for other people. Also my BPD was diagnosed a long time after I transitioned, my therapist before transitioning was too focused on me being feminine which she acted like was the source of all my problems and also she was a CBT therapist so no wonder it never got dxed until I saw a trauma therapist.
That said your therapist should not invalidate one just because of the other... I've complained about being trans and how emotionally hard it is for me countless times to my T who maintains that I am BPD and has never for a second questioned my transition and has said she'll do anything she can to help with it. And she isn't even familiar with trans issues so. I don't think they should be mutually exclusive, just, yeah the identity thing can also extend to gender confusion IMO... maybe it just hits an MAAB person a lil harder bc of not working well with the socialization people force on you. I don't really know.
Oh, also, my bf was reading this book about BPD and he said one thing that stood out to him that he always noticed from me was always having this nagging, constant feeling that other people think you are fake or wrong or whatever... so that affects being trans for me too. I never feel valid in my transition bc no matter how hard I try I personally cannot self validate. It won't feel right unless other people give me that validation. So maybe I really am trans and just constantly start doubting myself obsessively until people validate me again.
I guess what happened though was that transition didn't solve anyhing for me. I can't apprciate whether or not I feel better as a girl if i even do, all the ways I thought I would be happier didn't really help make me happier in the end. All I gained was one more way to feel fake and uncomfortable... sorry if that's not what you wanted to hear but it's just me :c
Edit (sorry for all the edits) one thing i also noticed is that when I see things glorifying being a boy now, esp a femme gay boy, I really want to be a boy again and it feels just like how I used to want to be a girl. So it feels like i'm just trying to fill an emptiness, not really identifying as these things, but I always end up doing that :/