Many things, none of which are particularly important as the feelings of the patient don't override the science of the sex. I haven't met a surgeon yet who planned a hysterectomy only to find out in the middle of the operation that the patient identified as a woman but was randomly assigned male at birth.

The history and an initial planned workup can be jumbled if it is not obvious which sex the patient is, but that is easily addressed once a physical exam or a more detailed history is taken, when they are important. For example, if you have a sprained ankle, neither your sex or gender identity alter the treatment for the injury. If you have abdominal pain, your sex and the presence or absence of various genitalia do become important in the workup regardless of your gender identity.