Well, weapon arcs make sense because of reloading equipment, ammo storage, gun weight, recoil dampeners, heat sinks (not to be confused with the ammo type), fuel lines/powerlines. And the big one: Cost. A gat will be cheap man, a heavy flak? Not so much.
Outside of game balance, the flak would be VASTLY more damaging than a simple gatling gun.
But yeah, I have no idea why the weapon placement on a spire is what it is. (The Galleon makes sense because, you know, port side. Docking equipment and etc.).
I don't understand the problem you have with the Squid engines. The current setup is probably done to minimize drag and so forth.
I think everything is pretty consistent, real engineers don't always make the best decisions. You ultimately do have to bow to balance, but you can come up with an in-world reason for everything that makes perfect sense if you look deep enough, just give Muse more time to flush out the background.