I don't know if you could say the walls look different considering it's from the same set. It looks less cluttered because they don't have those free standing gear
You can see some parts of the vertical shaft - a blade of a segment and a side of the connecting ring. But my guess would be either that the set was partially dismantled or that they didn't want to confuse the viewer as to which engine room (Enterprise or Excelsior) they were in and they didn't have the budget to make Excelsior's core unique.
The intermix wasn't partially dismantled, just kept carefully out of frame. The lower portion of what you outlined is one of the "rings" that seem to be a kind of connector joining segments of the intermix chamber. See my previous email -- they probably just didn't want to deal with the swirly effects.