From what I understand, it is just that they can't charge it while deployed, but Amex waives it as long as you are on active duty.

Honestly, the number of active duty folks using the lounges is marginal. I doubt it's enough to even be a rounding error. Most active duty military rarely use commercial air for travel as a regular part of their job and can't afford heavy leisure travel. I am sure Amex knows this. It's a nice benefit for military folks, so who cares?