@User: The conb cells are a known issue. . . they need to be changed from type

short

to type

sky130_fd_pr__res_generic_po

and have the third terminal removed. I believe this is the case with all of the standard cell libraries. I think that's the only issue with running LVS in your design. Since your "tempsenseInst_lvsmag.spice" file is a flattened netlist, then yes, it is expected behavior for netgen to flatten all of the standard cells in 6_final.spice since none of those exist in tempsenseInst_lvsmag.spice. If you want a full hierarchical comparison from netgen, then you need to generate a full hierarchical netlist from magic.