I also didn't travel commercial - I traveled "Space Available" on a MAC flight.
True, this was a decade ago, but I just had to show my military I.D. and sometimes my leave or TDY orders when I was trying to get onto a flight at a major MAC terminal like Dover or Edwards. Flying MAC through LAX, I didn't have to show my leave papers coming in from oversees, and only needed to show my I.D. to fly on to Travis.
Is he on a military flight or commercial?
When he's on orders, his I.D. doubles as a passport. Or has in the past
If he's coming in commercial and runs into trouble switching planes at SFO, he might want to check with SFO and see if they have some sort of military assistance desk. They might be able to pull up a copy of his authorization/leave order on DTS (Defense Travel Service) to verify that he is on orders.
I'm looking through the JFTR (Joint Uniform Travel Requirements) right now to see what he might run into; if he already has his tickets and doesn't have to leave the security area of SFO, he might be okay.
Here's the link if anyone else can find something before I can. Most of it deals with costs, but somewhere in here, there's the passport/orders regulations.
http://dodtravelregs.hqda.pentagon.mil/propub/template.htm?view=mainHaele