Those dark patches are probably some sort of emergency flush vents, since the nacelles on Oberth are attached directly to the hull. The nacelle supports on this ship are also pretty short, so I put similar vents on the back deck.
I one of those people who thinks the pod below Oberth is filled mostly with sensor equipment, despite what was shown on air. I designed both this ship and my earlier USS Paris to have swappable equipment hanging from a pylon.
http://www.starfleet-museum.org/paris-pods.jpg So, this ship can carry a pod like Oberth's too.
I'm leaning to having the nacelles sticking straight out, but angled up a bit might be ok. Decisions, decisions.