@User: Not at the moment. I was working on coding some corrections to magic's handling of substrate extraction which would have both fixed some issues with extracting P-wells inside deep N-well structures and also provide a way to isolate substrate regions in the layout, but the implementation has not been fully debugged and the 2nd MPW deadline came up before I could get back to working on it. So far, my best way of coping with this for LVS is to create a wrapper subcircuit or module around the top level that merges the two grounds together, and then LVS the layout netlist top level against that subcircuit. That would fail to catch any error in which you unintentionally shorted the two grounds, but it's the best I can offer at the moment.