Alternatively, what if there were four engine rooms? There were 4 lithium circuits that were blown in "Mudd's Women" and the ship in "The Alternative Factor" required 4 dilithium crystals to operate at full power.
One of the reasons that I chose to have all four crystals in one place (or one room) was because there was only one crystal converter assembly in both "Mudd's Women" and "Elaan of Troyius" suggesting a single point of failure rather than 4 different points that can fail.
Also, not all Season 2/3 engine rooms had the slide-up crystal holder. I think there was one episode that had some other rectangular device there instead. So you might need to have enough engine rooms for each crystal PLUS one more that doesn't have it. Am I correct to assume that in the engine room per crystal scenario that the Season 1 engine rooms are still also on the ship?