On second thought... this isn't just about this choice. It's also about what weapon loadout we give this ship. Do we want to invest in full coverage phasers as a priority? Or do we want to maximize torpedoes and phasers? I don't so much care about Cost right now, but I think given the ship's role I don't think we'd really be hurting it if we go with a central engine and focusing on phasers over torpedoes. At this size and given Star Trek's ship combat, she's not going to dodge enemy fire regardless. It's more about being able to fire torpedoes more often than anything else, with only matters in one-on-one combat encounters. And that's just not this ship's combat role.
Something else is, with only a central engine we still have 120% maneuverability thanks to the warp core plasma injector. But with dual engines, we don't benefit from that as we max out at 200% maneuverability. If the ship weighed even more than we'd have more mass for the dual engines to push, but as-is they're arguably overkill.
I think I've talked myself into voting for central engines. Huh.