Im not talking from personal experience, so might not be what ur looking for, but since Im into fitness and mtf myself I've always read on forums about mtf fitness that if you want to reduce ur muscle mass and get a more feminine body while transitioning beeing vegan is a good idea since u want to have high in carbs, good fats, and not too much heavy proteins... that way you are (after what I understood) going to reduce the masculine musclemass and start gaining mor fat which with the help of hormones should locate itself to ur hips, breasttissue and so on. I'm not sure about this, but this is what I've heard and read everytime I've looked into it. Therefore beeing vegetarian shouldn't be bad for transition if beeing vegan isn't.
But, on the other hand, those tips was for us who have a bit of muscle mass (my main problem area, too much gym hours in the past) and u said ur skinny. I would google it a bit moore, talk to a doc and se what they have to say. I hardly think it would be a problem, in fact it should by logic be good for you (at least I think) but don't take my word for it.
I really hope that it isn't a bad thing, I'm vegetarian too and I really dont want to change eating habits either. But I really doubt that's the case!