Yes and sometimes on the same job they follow it and ignore it. The ignoring parts come when they feel NEC requirements reduce security. (Think grounding or continuous metal pathways from inside a secure area to outside the secure area)
That said, I think it would be nuts to think someone in the Army Corp of Engineers* is going to put their butt on the line and opt out of AFCI requirements when the most all other areas of this country require them.
Think about it, put yourself in that persons position. Opt out of AFCIs to save an insignificant amount of money as a percentage of total job cost. No one is going to thank you for that.:happysad:
On the other hand if an electrical fire happens your career is kaput.
(*I am pretty sure it was the Army Corp of Engineers handling the barracks we did)