I'm not sure if we can assume their height in game is what their height in lore is. Often times in MMOs they need to make the bosses exceptionally big so that everyone in a raid can see and easily target them, no matter what race they might be. Which I believe is exactly what happened in the cases you've mentioned, if the moogles we fight along with Good King Moggle were normal sized it would be very difficult to keep track of them and tell them apart.