I forgot to include this morning that I think the reason why the Klingon crystal holder looks so similar to the Enterprise's is from this line in TVH:
SCOTT: We're ready, sir. I've converted the dilithium sequencer into something a little less primitive.
I figured since Scotty changed the dilithium sequencer it was a nice touch to have it look like he pieced the dilithium holder from another Federation starship.
As to the floor casing of the TOS Engine room being the energizer, I would suggest that it is more the top
of large energizer machinery that is below the floor. Kinda like how in TWOK that the crystals are on top of a shaft that leads down below to what I would imagine to be the energizers. I'd imagine that if Scotty in "Elaan" pulled the crystal holder out of the lift socket exposing the opening that radiation would probably pour into the engine room
Speaking of props re-used for "similar purposes" like the crystal holder, I think the most obvious one is the use of the TNG warp core in ST6. In ST6 it was never called the warp core or intermix shaft or anything yet we're okay to assume that it powers the ship...