Other than the HUD and ergonomic changes, are the NPC and player variants identical? Can CIG balance them independently?

The two ships are identical in terms of specifications at the moment, but you make a very important point: in the future, they will be balanced independently. This isn't to give players an advantage or disadvantage, but instead to represent the fact that Vanduul-produced Scythes will change as time passes, while the existing selection of human versions will stay the same (of course, when a theoretical Scythe Mk. II is captured, its abilities will remain for the player rather than it becoming an older model.)