My job requires a clearance, but so far I have only gone through a name change so my experiences may only be a portion of what you want info on.
From what I have been told from various sources (most I would trust), it's when you hide your previous names that the questions will arise. Despite you wanting only to move on with who you are, those doing the background checks more times then not will see it as you hiding something. If you list prior names then when they do the checks they will see you are being honest with them and that is always in your favor.
I don't know how detailed your checks would be, but in my line of work they will actually talk to people in your past, so if it gets that personal, you may wish to tell people whats going on and tell them that people you use as references or as family may (or are) not aware of your transition. The interviewers in most cases are contracted folks and will make sure they are sensative to your issues. The few I have spoken to were really nice people, though I was being questioned about people who have worked for me in the past....but they were really nice in giving me info on how their jobs work as far as them being contracted by a company to perform the checks.
Hope that helps. My advice is don't hide anything because it could hurt you more then help.