Is Magic extracting a different .gds to the one that Openlane creates at

caravel_user_project/gds/user_project_wrapper.gds

?

It shouldn't, although that doesn't mean that it doesn't. Openlane takes a DEF file output from OpenROAD and uses magic to read the DEF and convert to GDS. It can also use klayout to do the same thing. As far as I know, the script using magic is the one that is generating the final GDS in openlane. The DEF file contains only subcells, contacts, and wires, and so there isn't a whole lot that can be different. That said, there have been occasions where I incorrectly implemented an obscure and ambiguous point in the DEF spec, so it can happen.