@Mitch Bailey: FYI, the push cited above contains all of the corrections needed to get an LVS clean result from the SkyWater I/O pads extracted in magic. This gets rid of the need for all of the "hack" solutions. Please see the file (in open_pdks)

sky130/custom/scripts/gds_import_io.tcl

. This is the recipe for (what I think is) a minimum set of wildcarded cell names to flatten on GDS read-in. The views in magic are then correct for extracting to a netlist and passing LVS. Note that there was also a fix I made to netgen to resolve an error with disconnected pins which may have been at the root of the proxy pin issue. The problem was that when a subcell had a disconnected pin and was flattened, there was no check to see if that pin had become disconnected in the parent cell. Without that check, netgen will flag a mismatch between the pins.