Back when I was a GS-2210 for the U.S. Gov and traveling a *lot* overseas for the wars, going through customs in the U.S. was cake.
"Sir, what's the nature of your trip?"
[show blue passport]
"What kind of government work?"
[show military ID]
"The kind you aren't cleared to know about."
You show a military ID or brown government passport and TSA tends to STFU and let you go on about your way.
I remember the really old days when we traveled with TWO blue passports - one for Israel and one for the Arab states so they wouldn't know you've been to Israel via transfer in Frankfurt.
Man, talk about racking up the frequent-flyer miles!