Well, I am a total mess, but that's another story
The military (and other Gov't agencies) have "executive aircraft" that we the taxpayer, are already paying for
These aircraft are as nice, and in many cases, nicer, than commercial aircraft, and could be used without incurring additional taxpayer cost.
Cost aside, even using commercial aircraft, why not simply have them land at a military facility, pick up the troop once they've been cleared by an appointed offical within thier command, transport them wherever, then land at another military facility.
No civilians involved (other than the flight crew), they go point "A" to Point "B" where they'll be debriefed, medically cleared, etc (any outprocessing they need to do) and are reunited with thier families in private!
By having one person (or team) designated as the Customs POC, you have a single POC and total accountability for the troops, without subjecting each and every one of them individually, to the rediculous TSA BS in public!
By using this method, it's no different than having a captain held responsible for the actions of his/her ship and crew.