Yes, but "could" is the operative word.
Along with "proportionate". How much time is this transman intending to spend in there? If she was planning to camp out all day, that's one thing, but if she was just passing through, then anyone who does have a problem can wait until she's gone.
If you're talking two regular patrons where you've got one transman and one other woman who can't cope with her there who will be frequently encountering each other, then you've got a continued conflict so the establishment's going to have to come up with a solution to separate them - an additional unisex or private space.
It can be explained who they are and why they are there.
Who knew therapy was so easy? You just explain things. Job done.
Also wondering how far this goes - if someone has a clown phobia, do you let people turn up to the same session in clown suit and makeup, and just explain "they're not a real clown" and why they've turned up like that. (Why?)
Not turning up to a group therapy session in fancy dress that might upset people isn't a huge ask. A transman is making a conscious choice and significant effort to try to look male and project as many male cues as they can. If they want to join in with other women, then they can give it a fucking rest.
But in practice, yes, most women aren't going to have a problem with a transman, so usually there won't be an issue. But a phobia against someone with too many male cues is not unreasonable, so again, some form of separation will be required.
And the SC judgment made clear that asking the transman to join another session would be permitted gender assignment discrimination. Up until the judgment the assumption/convention has been that the trans-identified person always gets what they want in the presence of a conflict, and the non-trans-identified person would have to find another space (which may not exist).