My wife is also trans; she said no to that question, and didn't run into any issues (currently at the portal 1 stage). We did mention her transition in the LOE.Regarding the Schedule A / background form :
My wife is a transgender, going MtF. She is on hormone replacement therapy for more than a year now. Does she need to say yes to "do you have a serious disease or physical or mental disorder" and explain that she is a transgender? This is a very delicate area for her as you can imagine, but I know it'll show up during her medical exam.