Do you think these questions should begin a Federal Employee Survey that asks how the leadership are doing in the work place?

What's wrong with those questions? I don't see the problem. If you're transgender say yes. If not say no. If you're none of those orientations say "something else." If you have a disability answer yes. I fail to see the issue.

Considering how issues related to these come up in the federal workplace, no reason for them NOT to be there.

You're not obligated to take the survey. They kept pestering, I kept ignoring. Problem solved itself.

Consider what these surveys are for. They are data mining for the purposes of crafting training for management and workers.
Answer honestly, and they have better data with which to work.