I got in touch with GenesReunited today and asked them for a recommendation of the issues of transgender in their family trees and if they would consider an option for those who have changed gender.
Their response is that you should either:
a) Add your gender as it is on your original birth certificate
or
b) Alternatively add to the notes section on the family tree mentioning that you have under gone gender reassignment.
I personally opted for (b) and added notes, but then the problem arises when you need to add a previous partner and children as you can’t add the same sex partner, hmmm. But as my kids and ex and disowned me and classed me as some abomination, It doesn’t make any difference, but suffice to say that the lost relatives I have found are great 
If you like what you see, buy me a coffee!