Okay, Ive confirmed that the engines, navigation, bridge, and weapons are effected by this. Its being resolved now and will be fixed soon.
I would like to point out that regardless of Zanes over the top reaction, the subs are not "so far out" from the hull, and that the positioning of the special point of the engines is pretty much the way they had it in retail, save a few critical meters that caused the error. Here are some shots for proof:


So this sentence: "The engine subsystems aren't even pointing to the thrusters, instead they're placed on solid hull above it" should be directed at Volition, because that is the exact way they had it.
If anyone would like to dispute this, do what Zane apparently has no ability to do: compare it to the retail.
I take responsibilities for the bugs, and I'll fix them. But Zane, when you place that "hang em out to dry" attitude in your reply, it gives me half a mind to just leave and say screw it, to hell with all these damn whiney users. When using phrasing like "so far off" and "aren't even" you give the impressions that there was some HUGE mistake that should have been obvious.
Anyways, its being fixed.