Its an airdock. Now why its between the engines is easy to explain:
First you load the dock with Advent prisoners. Seal the dock, open the hatch. Watch them get sucked out into space, which happens to full hot whatever coming from the engines. No better way to burn the witches in space.
Im thinking that door is there for servicing the engines themselves. I imagen the parts are quite massive so as wouldn't fit in other parts of the ship. So if say they on of the generators died, that door could possible open right into the engine room and let them replace it.
I dont know what kind of Kol's you use but my Kol's never breakdown, fail, or die. lol
