I'm seeing the same issue. I want to modify the inset on some inner screw threads, but not on the outside of the model. I placed a 5mm tube around the 4mm threads, used per-model settings to set an inset of -0.4 and nothing changes.
I then tested by expanding the tube to cover the entire model, and set the insets to -4. This should basically wipe out my entire model (just a 5.8mm tube with threads). It has no effect whatsoever. But if I change horizontal inset on the base model I get the expected results.
Screenshots attached to show each case. The per model settings result in identical slices.