Indeed. The transition phase is the most complicated to deal with.
Most people, including everyone I have ever heard express an opinion here at ISF, would say that a person who has undergone a sex change operation (to use an old fashioned term) should use the facilities associated with their newly approximated anatomy.
However, there's a fairly long period of time in preparation for the surgery where, there's no doubt about it, things get a little odd. At what point does it make sense to say that a person really ought to switch sides at the gym? I don't have an answer to that, and would defer to people with more knowledge of the transition process. Most people at ISF, and I think the majority of people in society at large, would be ok with accommodating people in that situation. If those were the only people we had to make decisions about, there really wouldn't be a huge problem. Threads like this one would be much shorter.
The issue comes in when the trans rights faction insists that people who have not begun the transition, or who have no intention of ever beginning the transition, get treated the same way as those who have transitioned or are in the process. Before the transition, there's a word for those people, and the word is "men".
And when it comes to sports, even post-transition it doesn't make sense to treat trans-women exactly like the non hyphenated variety of women.