give all flying creature a creature_class:flyer and all not-flying creatures a creature_class:ground, and then have the machine gunner only target "ground" and the anti-air only target "flyer". I think that might be possible.
Is that possible? That would be pretty cool.
Then I wouldn't have to worry about the CIWS (What I am using for anti-air) being overpowered. I don't have the explosives worked out like I want for an immobile unit like the CIWS, but if I could get a slade machine gun up, it might work like I want it... Kind of difficult to do though?
I am really surprised you keep dwarves and goblins in it... this sounds more like humans against humans of other nationality 
It is still a fantasy mod. Its just now instead of having dwarfs and goblins fighting with swords and shields you have dwarves and goblins fighting with guns and tanks. Still have dragons, giant tanks, necromancers, humanoids with healing factors, and annoying hippies. Its dwarf fortress, if it had been set in a modern setting.