Continuing my mini-series...
Someone in Starfleet really wants to see his or her ship designs fail easily and in spectacular explosions. There is no other explanation for the fact that the warp engine pods are projected out from the protected main hull on thin and likely weak struts.
Not just Starfleet. Everyone else in the known galaxy places the engines well clear of the body as well. Except for the Borg, but then again, the Borg are the exception to a lot of the ship designs in Trek. That's not particularly difficult when your ship is a cube of hobbled together parts.
I see no reasonable justification for placing the engines in such a vulnerable position. There cannot be environmental issues as in the shuttles and some other ship designs (not many) the engines are placed in close contact with the hull. And even if it were emitting deadly radiation, there's a thing called 'shielding'. I'd gladly trade a small loss of energy or weight to shielding than place the engines outside with bull's eyes painted on them. For the same reason, propulsion does not seem to be affected by distance from the ship as some designs place them close if not outright attached to the ship.
Maneuverability isn't a factor, as it's the warp drive. If you notice, the ship orients itself before engaging warp. I can only conclude it operates in a strict unidirectional fashion. Similar to a motorboat without a rudder. In addition, some designs have only a single engine pod. If two very exposed and distant pods were required to 'turn', these one engine designs would be unviable. And those engine pods don't rotate to thrust vector, either, because I've never seen that occur. Ever.
Since all you need is a single engine pod, which appears to have minimal environmental and maneuverability impact, I would have the engine encased within the hull of the ship rather than outside and exposed on stilts. You could hollow out that secondary hull (after getting rid of the unnecessary civilians) and place the engine right inside of it. It'd be snug, secure, and in the event the shields fail (as they are wont to do) there is an added layer of protection in the hull of the ship itself.