{Edit} Ah, I see. You were complaining about the secondary Hull, and not the main. Okay, so... some things. One, we don't currently know how much space would be required width, nor length wise. We only know that the minimum deckage is 4 for the reactor. Which would be rounded up to a 30 meter hull height, at a minimum... if not 35 to 40 for extra. Cargo would likely pad out the width and length by a good deal. Though I'm at a loss as to why sticking a large cargo pod engineering section straight out the back would lose us a warp factor... Since without the deflector on/in it, there's no reason to drop engineering below the Orb. And even if there were a reason for the performance drop; there's no reason we couldn't stick a third nacelle on top of the engine hull and drop the other two below (for emergency core ejection if needed) to recoup. Or am I reaching for something I don't understand @Sayle?
Each deck is 3.5 meters. As for the huge cargo pod, warp dynamics. Huge is huge.