I can speak to this a little, the issue is that the sets are designed to not be as friendly to rebuilding. The walls and floors to buildings are made out of very specific pieces that aren't easily reconfigured into new structures.
Honestly some of it is so weird that I think they do it on purpose specifically to discourage re-use.
I don't think this is true at all. I recently built the Saturn V and the Mario Question Mark Block and neither had _any_ notably unique pieces in them and certainly not in any excess quantity.
Honestly some of it is so weird that I think they do it on purpose specifically to discourage re-use.