its just a name so I see no reason why this is an issue.
as for the flag thing:
-25 commander dragon flags (assuming I can math) result in about 108,250xp (25 games, 1000xp/game, 83250 from flag) adding the additional 75 games with base xp you get an extra 75000.
-100 regular commander flags would be 150,000xp (100 games, 50000 from flag)
not to mention that you get the bonus xp in a quarter of the time. I would rather have 25 dragons to 100 standards.
ship modules shouldn't be part of the drop pool though, since they are ship specific. Flags are reasonably universal so anyone can find them useful.