In practice, I think the admittance of transwomen could be an issue if a transperson was pre-op, still had male genitalia or dressed and acted as male. Because, to the people they interacted with, they would be male.... Identification is a negotiation, not a given...and we require validation and acceptance from outside ourselves because we are social animals There is no hierarchical preference between women and transwomen but power relations between men and women are not equal...and appearing male, to all intents and purposes carries more weight than what is under one's shirt and within one's brain, in such highly charged situations as a refuge.
Having worked in one, there has always been some power to remove or segregate - to maintain a level of safety and security within the wider group, disruptive or violent women have been excluded.