Ah, I see. Unlike the device models I needed to have the logic cell spice libraries explicitly included (they were only included in the top level simulation file). It matches now! It looks like there is something in the sky130 setup file for netgen that ignores decap and other cells that is not implemented for the HVL library, but there are easy enough workarounds

That's odd. The setup script is doing a regexp match which should match any library cell that starts with

sky130_fd_sc_

and so is supposed to work on all of the standard cell libraries. It ignores fill and tap cells, but not decap. If you need to ignore decap, you can copy the setup file locally, uncomment the lines that tell netgen to ignore decap, and use that setup file instead.