I can work around it with some rmetal, but it seems that using multiple ground rails in different designs results in consistency check failures because they "short" together through the substrate, which makes magic extract only one port

@User @User did some work with multiple ground substrates by adding a separation layer to the layout. I'm not sure if those changes are incorporated in the current magic tech file or not. Yeah, it looks like it's in there

isosub 81/53

. Maybe try adding that around your regions with non-standard ground.

Yes, that's exactly right. Ask me if you have any specific issues with the layer, but generally speaking, you just want to draw an "island" of "isosub" under the entire ground domain that you want separated from the rest.