He addressed this issue in the OP. It's recommended that you select the sex assigned at birth, or closest to it, even if it's not the gender you identify most with currently. So male-to-female transgenders should select male, female-to-male transgenders should select female. And if one was born intersex, than they should select the sex they were closest to, whether male or female. I'm not sure exactly why they opted to conduct this survey like that, but I thought the instructions were pretty clear. Whether or not you personally agreed with them was another matter, though.