*checks internets*
Stargate..oh, that tub..nope, they don't look a like.
As far as your other points go:
I'd rather have a thick, long and armored corridor and several extra slabs of armor in between, just to be sure...like I have.their not close to safe, if the reactor goes, everything could go. right up to the bridge. it NEEDS to have the long connector.

Well, if it's thing, has a corridor running trough it and all essential weireing..that doesn't leave a lot of room for armor..unless you throw in handwavium.well first off the ship has a lot of armor on all the sections, just cause it looks thin doesn't mean it is, but it also needs to be light so it isn't loaded down. but remember its not the engines that are dangerous, its the reactor systems. it also has engines under the wings (powered via the large conduits visible in my bpo) all the engines have one time use fire and pray battery systems, that hold a large energy reserve capable of blind jumping the ship in an emergency, so losing the engines doesn't doom the ship.
Speaking of which - how do ships jump/travel? The jump drive/hyperdrive/slipstrem drive/whatever surely needs a LOT of power and some room too. Stored energy sounds o.k., but realisticly speaking, one would need a LOT of batteries, since fiddling with the laws of physics is very, very hard work.
and yes..I'd still rather separate then just blow up the hallway.
About the weapons - when making blueprints you have to account for that - where are they located..how does a mechanic get to them to repair them..where do the power lines go, how is ammo fed to the weapon.
If there are turrets then there must be a visible way for a gunner to get on and man the turret in question.
Handwavium.actually their designed with high intensity inertial dampening to stop cargo movement, this provides a strong amount of armor resistance and allowing it to act like a bullet shield for the habitation area.

Gotta remember to make a wall out of my suitcases the next time someone fires a ICBM at me.
