I get where you are coming from. These are definitely uncharted genealogical waters.
The difference here, from a woman's maiden name, is that a person who defines as transgender, as fully transitions to their true gender, is considered and considers her of his self as having always been that gender, from birth, regardless of physical characteristics. Gender can be defined as a mental, not physical state. This is medically and legally being recognized-- with legislation being passed to help transgender individuals amend their birth certificates to reflect their gender, it's something that we will be faced with in our family trees. In this instance, amending a birth cerificate for gender would be more correcting the birth certificate to the gender the child was all along, rather than amending it for an adoption, etc.
If this is a living person in your tree, I would expect that she or he would be greatly offended to be considered the gender assigned at birth, as this is contrary to everything the person believes about his or her self. If this is a recently deceased person, I would imagine that friends or family who supported this person's journey would likely become very offended at the listing of this person as their originally/physically assigned gender.
If someone legally transitions to their true gender and passes, the gender listed on a death certificate now would be the gender transitioned to.