I'd go for Option 4. The humpback has qualities of the deuterium tanks envisioned for the Enterprise-D, though I'd imagine the antimatter pods to be located in the bow part of the humpback.
Reason for this speculation is that during a head-on confrontation / attack the neck of the Excelsior, the saucer hull and the protruding impulse engine section would probably serve as a good mechanical shield protecting such antimatter pods.
Another reason is the obvious design similarity to the engine pod of the Oberth Class. While I believe we are essentially looking at a pre-TOS design with the Oberth, I have no reason to doubt that the humpback on its engineering pod is a mid-23rd Century upgrade (or a genuine mid-23rd Century design for those that disagree with my theory).
But regardless, I think any theory needs to be compatible with this screenshot from ST III
, and the images we could see before (didn't we see part of a vertical intermix shaft?)
The TOS references in "The Apple" and "The Savage Curtain" only suggested the discarding of the warp nacelles while in "That Which Survives" the ejection of the "engineering core" in the engineering hull seemed to be the solution if all else failed.
On the Excelsior
it would appear you could do both if the necessity ever arose. You jettison the humpback matter-antimatter module and/or the warp nacelles.