Having the nacelles means that the release of “plasma” doesn’t hurt the rest of the ship. I can understand that. I can understand that the shape of the warp field can affect how fast a ship can go and what not. Having separate hulls for living and work quarters and then engineering (storing vast amounts of deuterium and antimatter, at that) makes some sense, although if there were a true accident, it may not make much of a difference.

But then, it really seems that there is plenty of wasted space that could actually having something there. A skinny neck connecting the disc to the engineering hull? That makes no sense.

And in this case, the protuberance below the engineering hull is really quite a WTF. Also, it’s space, so why make it look aerodynamic?

The exterior shots make it look like it has four warp engines, but the internal schematic only shows two.

And that’s one hell of a secondary craft that it carries. Three stories high.