In my experiences with the health care system if you're trans you're but into a different category medically speaking. Since a trans man that's pre-op would have the internal organs of a woman BUT he would be running on testosterone, many pharmaceuticals react differently based on hormones NOT chromosomes so it's important to not treat them like cis woman, or a cis man.

Because they don't have the hormones of a cis woman or the internal organs of a cis man so if you prescribe drugs you can expect the Testosterone based 'side effects' that showed up during drug trials to appear, but you'd need to give them a pap smear every once in awhile and not go looking for a prostate.

If you're just putting them in the male/female box you're fucking up your research and it's best to just have 4 boxes Man/Woman/Trans-Man/Trans-Woman (If you actually want a sample size including all 4). No trans person with any basic medical knowledge will get pissy about being put in not man/woman category because it's very relevant at times to be aware that

"This person runs on estrogen, has breast, lots of other secondary female sex characteristics and a prostate etc"

"This person runs on testosterone, had a mastectomy, hasn't had a hysterectomy so has all those female internal organs and doesn't have a prostate etc"

It's just best practice to make a new category because it's rather obvious that for medical studies male/female isn't going to work. But again very few studies even care to devote resources for including non cis people, since generally they're not funded enough to bother using resources on the minority of people who fall out side of cis-man cis-woman.