The latter would be a nice mirroring of what happened to warship propulsion between WWI and WWII: the expensive battleship hulls were refitted with new powerplants that were one half to one fifth the size of the originals (while being vastly more powerful and fuel-economic), and some modern superstructures were also applied, but the fundamentals stayed the same.
Okay, to use that yellow roundel as an ejection port, one would need to eject something else than the vertical core, because that one can't go through the cargo area. In my first pic, the yellow hatch ejects antimatter tanks, while also theoretically providing access into the cargo area; perhaps that's consistent with the TOS-R treatment of the hatch in "Operation: Annihilate!", too? It might not be possible to eject the vertical "warp core" of the TMP ship any more than it is possible to eject the identical horizontal structure. So perhaps the only thing that is ejectable is the antimatter storage (much as in "That Which Survives"), or perhaps also the dilithium reaction chamber that sits somewhere down there.
And perhaps the E-A thick structure is placed above the yellow roundel then, replacing the original reaction chamber (because that's what it is in TNG, too) and occupying much of the cargo area (because it's an experimental new design being tested here on this old piece of multiply refitted junk) but still tying to the original power chain (hence the vertical plasma conduit that is in the style of the TMP vertical and horizontal conduits - it just ties into the general conduitry a bit differently on the E-A).
For the TOS ship, there'd be a similar reaction chamber somewhere deep in the bowels of the ship, too. And in TOS and TMP/ST2 ships alike, dilithium would be taken to that heavily armored reaction chamber via a dumbwaiter system that terminates in a heavily shielded floor hatch in one of the control rooms...
As regards the hatches on the E-A bottom, should we think that the TMP ship had those as well, only not color-coded? The surface finish of that vessel was different: perhaps she had been given a stealthy coating that had to be smooth and couldn't feature seams for these extremely rarely used emergency hatches?
As for the red square in the fantail undercut, it doesn't look much like an opening hatch. Unlike all the others, it's merely a set of lines drawn across the hull seams, and even across a major hull bump of some sort. Perhaps the role of this red outline, and of all red outlines on the ship, is one of an approach tracking aid? One would need that, perhaps, when docking with the aft shuttlebay or the ventral ejection/cargo hatch.
Timo Saloniemi