@Bob - In "The Alternative Factor" it is possible that the crystals were "re-amped" somewhere else and placed in the "energizer" once fully amped. However, since re-amplify was tied to the amount of energy in the crystals and it required an energizer or energizing equipment I think it is simpler to say it all happened in the energizer.
As to "The Immunity Syndrome" engine room, it depends on if you think we saw different rooms at different times or the same one at different times as to what features it has
As to the multiple engine rooms in the engineering hull, I figured there must be more than one. In the WIP, I placed them staggered in order to accommodate the width of the forward hallway in a 947' hull. If they were side by side, the EMM's would be next to each other and that would push the starboard turbolift potentially out of the hull.
The bypass/converter assembly I think is going to be interesting. If there were 4 engine rooms with 4 crystals, then the converter assembly would have to somehow be connected together to function as one unit. The sticking point is still the rooms with the black box instead of the slide up paddle holder. Did those rooms show up only prior to the appearance of the slide up paddle holder or did they also appear in episodes afterwards?
Or are you suggesting, a dedicated bypass/converter engine room that has the only
slide up paddle holder that services the four dilithium paddles?