Notice that my response to you was measured, that it didn't assume you meant harm.
You asked a worthwhile question, though loaded with some extra baggage, but I still trust that you meant no harm. Ours is a culture of irreverence and making jokes at the expense of others not present is not only acceptable, but rewarded at every turn. It isn't strange that you would try to make a"funny" comment at Jenner's expense, and I'm certainly not going to go out of my way to hold it against you. I will make sure that you are aware of the actual etiquette, though, so that you don't mistake a cheap shot for an appropriate form of address to use with regard to a future patient, or colleague, or someone else who deserves better from you.
With that housekeeping aside, to answer your points:
You don't know females with identical applications to males. Even if their stats are approximately the same, they didn't write the same essays, have identical ECs, apply at the precise same time to the same school, or interview identically well. They didn't demonstrate identical personal characteristics that go beyond the numbers. There is no shortage of high stat individuals to admit to medical schools, so that there is no reason for schools to need to lower the bar to get the right number of either gender into seats. There will be some variation in the actual numbers of MCAT scores and GPAs of admitted students to a particular school, but they are all going to fall within fairly narrow ranges. There are many factors that go into selecting which individuals from within a pool of applicants with given stats actually get seats. Gender is only one.
As for how a transgender student would "count," it would probably depend on what they put on their app. Any school that is going to play gender police and decide which grouping a student "really" belonged in is one that is far more likely to just avoid the controversy by moving along to an applicant that doesn't cause them to have to make that determination. I didn't talk about my own gender in my app at all. I did discuss wanting to make a contribution toward better access to care for GLBT patients, but I didn't feel the need to waste precious characters discussing irrelevant personal matters. Everyone has coming of age stories, and they might be very interesting indeed, but the PS is about why you want to be a doctor, and I had more cogent things to say about that directly. If my school wasn't aware they were getting a transguy as a student, so much the better. They got a little extra diversity thrown in for "free," no need to do anything extra to make it happen.
I'm hoping your thread doesn't get deleted... and that it doesn't turn into a dogpile. There is absolutely room for civil discussion regarding these topics.
One reason that I am so vocal about being transgender is that we are health care professionals, or going to be someday, and we will encounter patients who are transgender, or gender nonconforming, etc. Those patients deserve to be cared for by people who have at least given serious thought to an issue that so greatly impacts their physical, mental, social, and spiritual well-being. Even if we come to different opinions regarding these issues, they deserve to be given meaningful consideration, beyond crude jokes and celebrity gawking. Although this discussion started out a little rough, I thank you for opening it up. I hope you will come to appreciate its value as much as I do.