I believe, in most cases anyway, we will be dealing with living people in regards to the transgender issue. So, as Anonymous puts it, we should just ask for the individual's personal preference!
The main problem will be when adding family - spouses and children mostly - since the site is currently geared toward the traditional "father/husband is male, mother/wife is female" mentality. Eventually, we will need to address this issue, hopefully making WikiTree the standard for inclusiveness!!
Whatever we decide, remember that the gender box is flexible and can be changed. Also note that it's not specifically set as "gender at birth." So pass these tips on to fellow members!