I figured it was all there all the time. I always thought that the paddle-shaped crystals seen in the "Alternative Factor" and other episodes were used for specific applications in different pieces of equipment throughout the engineering systems. So there's no reason why it couldn't still be there.
In my own arrangement, I put the "Alternative Factor" room in the saucer as part of a separate power generation facility. (For what it's worth, I but it below the sickbay, linking two engine rooms in the saucer.) I was thinking of the saucer a separate vessel from the engineering hull since it was meant to be a lifeboat in emergencies. However, the more I think about this stuff blssdwlf
is doing, the more I like everything about the layout.