From the netlist you show (I assume this is the source), there are two pins. You say: "So they touch each other in the GDSs." I assume this means pinx and piny are shorted in the layout. Assuming that's true, the connectivity extractor will only extract one pin in the layout, and there's no way to override this.
I think you've got two choices. Either your source netlist above is correct, in which case you need to split the physical pins in the layout so they aren't touching, or the layout is correct, in which case you need to make your source netlist look like the extracted layout netlist for the macro in question.