I am doing a research paper about the above subject and am curious as to your response. Suppose a person has been diagnosed with gender dysphoria, and they dress daily in the clothing of the opposite gender. Specifically, someone who is biologically female but for all intents and purposes looks like a man. What are the problems that would arise if such a person wanted to daven on the side of the Mechitzah according to their dress, and their identity?

Shalom U'verachah, It is hard to give a specific answer to your question, but generally I would say that a man should sit with men and a woman with women despite the way that they dress. Of course in a specific case we would have to see how to help the person so that they would dress in an appropriate manner. Kol Tuv