On the subject of why the warp engines have to be so far away from the power-generating reactor in the interpretation where the engines themselves aren't power-generating potential bombs...
Perhaps it's in some ways analogous to the relationship with seagoing ship powerplants and propellers again? Those generally aren't in the same place due to concerns about the center of gravity: the long propeller shafts (or the long hydraulic leads, in case the props are on rotating pods) are there to allow the massive power systems, and to some degree their fuel stores, to be placed close to ship centerpoint.
In the Star Trek case, it could be that the reactor isn't particularly massive yet the fuel sources still are. The nacelles have to be in an outlying position for the same reason the propellers are: their function calls for exposure. But a stability concern of some sort, perhaps relating to impulse drive, calls for the fuel tanks to be at the very center of the ship. That's where their constantly changing (that is, decreasing) mass will have the least effect on stability, at any rate.
Once that's decided, the accessibility issues are in synch with the need to have the reactor close to the fuel in its volatile antimatter form; the leads of the less dangerous plasma can be made longer to compensate.
Not that all known starship designs would conform. But we don't have blatant counterexamples of the fuel being far away from the reactor, either - except perhaps in the Oberth
class, in the model that has the reactor up in the primary hull and the fuel down in the pod. (And that's not the model that the Okudagrams support, to be sure.)