Cruiser Command

As the title suggests, it appears that the lower deck is flipped in the opposite direction of the upper deck. It looks like the engines are on the north side of the lower deck, but on the south end of the upper deck.

south on upper deck is power core, not necessarily engines, and the bottom deck is not flipped :p exactly what north on bottom deck is still a mystery :p but, If i had to guess, it might be the main conduits from the weapons and nav consoles, maybe the drone antenna :p however, i believe siretu has some specific plans for that unused console, that will make that interesting tower (which i first thought was umbilical from power core) make more sense once he implements what ever secret lies in wait at hat spot ;p

It really looks like the engines on the north end of the bottom deck that are on the wall.

My suggestion: think of it as if the miner packets are coming in at an insertion point at the bottommost part of the ship, rather than the backmost. Also where the infiltrator comes in.