I truly hope this is a minor issue. My three sons participated in Scouting overseas on military bases, much to their benefit.
The only thing that could change is that the official sponsorship for the troop would go from an "official" military intenty (if there is one) to a "non-official".
In other words, if they were the Fort Myers Troop they might become the Fort Myers NCOA Troop (sponsored by a non-official entity).