Yep, that's the problem. I've thought it over, during the night. As I see it, if they are all female, it will be because of lack of male applicants, not any principle. MW worked there for years and that will have shaped their policy on the matter.
If your friend's opinion on whether TW are women is relevant to what she's seeking support for, she would have to watch her words to an extent that could destroy the therapeutic relationship.
It's reasonably likely that they are thus currently female-only because MW was fond of describing self as the only transwoman of colour in the Scottish women's sector, but this means they are female by default. The moment a male person does ask, women lose their services. We saw what that meant in Brighton, when the rape crisis service allowed a male to attend the women's group discussion.
At the end of the day though, it is still worth asking them if they can point you to specialist sexual violence support in the area for your friend. They describe themselves as having 35 years of experience offering domestic violence support to BME women. (Their wording not mine.) When you follow up with their recommendations, those might well be female only.