Ending discrimination is great, but that's not happening today. And today, people need to cope with discrimination. Which sometimes means singling out people who are discriminated against, using the same criteria that the discriminators use.
Trans women face discrimination in many of the same ways that cis women do, and in most circumstances it's best to simply treat them as women. There are a somewhat-nebulous set of cases that should be restricted to cis women, but much of the time those cases are more about anti-trans-discrimination than actually protecting cis women in particular.
Any case of discrimination for the benefit of marginalized groups is going to invite scrutiny, and sometimes legitimate disagreement. It sounds to me like this case is reasonable to exclude men, but not to exclude trans women. The fact that they don't menstruate, for example, doesn't mark them as non-women: lots of women don't menstruate (young, old, ill, athletes, anorexics, etc.) It's true that many lacked girlhoods, but increasingly many have transitioned at a young age.
That's my cursory opinion. It could change if I were exposed to more details.
But I don't consider it helpful to say "to end discrimination we should stop letting people self-segregate". That attitude fosters abuse by people who discriminate, and forbids people from protecting themselves against it. Maybe in the future it will be helpful, but today it harms a lot of people.