Many years ago the company I worked for was taking on some DND contracts which required everyone to have a military security clearance. The form required a 25 year history which, for me, included pre-transition.
In the space for "any other names" I wrote "information available to authorized investigator only". I did get a call from a high ranking officer asking for an explanation. I told him the whole story. He was very understanding and went to great lengths to preserve my stealth, even using proper pronouns and names in every case. No one was ever the wiser.