Yes, we're definitely getting there now. The tweaks to the nose and tail are just what I was thinking of.
Hmm... I like the shape as it is, and given the more linear design, I think we could justify it being somewhat longer than Serenity, so long as its volume is similar to that ship's interior spaces minus most of the cargo bay. So maybe you could up the size a bit more. 85 meters?
On the other hand, I think a full deck/half deck arrangement could work, though it would require DEWLine to do some rethinking if he wants to combine projects with yours.
Hmm... what if you made the top slope a little more gradual in back? That is, the contour from the highest point of the ship to the rear is a little bit concave; you could make it slightly convex, or at least have the downward curve start a little further back. You could add a few meters to the upper half-deck that way.
As for "engineering," I don't know if we need a whole engine room; I'm fine with an alcove at the rear of the corridor with some basic control consoles. We don't need a visible warp reactor in the middle of the room. It could be behind the wall or under the floor. In fact, the main engine controls are probably on the bridge/cockpit; the engineering area would just be a place to monitor the engines and occasionally get in for some fine-tuning and direct maintenance. It would normally be a one-person station, if that.
By pushing the overall length to 80 meters, we get just shy of six meters from the bottom to the roof of the impulse engines without having to adjust the curves. With conservative deck heights and framing space between decks, I think we can squeeze in a full deck top and bottom with an in-between "split level" deck extending into the nose cone and above the navigational deflector that should be perfect for your cockpit/bridge. And creative use of short spaces will also enhance the submarine feel of the ship.
Now, regarding the smudge locker, your thoughts of a jettison-able antimatter pod are on the right track. Consider: Picard approached Centauri III's manufacturers with a specification for extreme-range operations. By modifying an existing design -- the courier/scout you mentioned -- an acceptable vessel was found, but the extra range at high warp required a better reactor core and a larger supply of antimatter. The upgraded reactor displaced some of the available space for antimatter containment so a pod was designed and attached to the hull. Containing most of the ship's antimatter, the pod can be jettisoned in an emergency, leaving the warp core with small, short-term supplies. The warp core itself can also be jettisoned along with the supply pod.
The antimatter pod's shape is defined by the vessel's standard warp field and it looks like an afterthought because that's precisely what it is. Obviously this is a bit of a tactical weakness, but the ship isn't intended for combat, and just because the tank is exposed, doesn't mean it isn't heavily armored in case it gets shot while the Cleo
is fleeing. We'll paint it a different color and possibly rib it externally to suggest excessive reinforcement.
I don't want to add any further details to the hull or make any more tweaks until we know for sure this shape can accommodate your mission requirements. I'll mess around with cross sections and see if I can come up with suggested use of the available interior. Maybe before we're done, we'll have an interior set to go with the exterior model ... but I don't want to get too ambitious.