We're not going to change the terrain to simulate space. If that were the case then this wouldn't be a ground combat mod, it would be another Armada mod, or a Heagemonia mod or some other space based game. Like you said, Generals would be all wrong for that sort of mod.
You're also right, however, in regards the Trek units. There aren't that many to choose from and those that are known, are set in the Original Series timeframe (ie, from the game ST: New Worlds). The thing about this though... it gives us complete creative control
Sure it means the mod will deviate from the cannon information, etc. but if it balances the game, all the better IMO.