I think the queue at TDS is adjacent to the ride, not really above it (except at load).
It definitely is possible to retrofit the Dinosaur building to create the open cavern scene, but it would likely be expensive.
The walls separating show scenes are almost certainly not structural (I feel like shear walls wouldn't typically be so close to the center of the building, but I am not a structural engineer). But there probably are structural columns in the middle that would need to be changed at significant cost.