It depends what you want to excite.
If you want the network parameters of just the microstrip mode, the wave port needs to encompass these modal fields; i.e., between the microstrip and its conductor backing. If you want some supermode that encompasses both the microstrip mode and the PPW mode of the power layer, you would want the port to cover all of these layers.
However, I note that you've used PECs in your simulation, so there shouldn't be any coupling between these modes. So I think your simulation setup as presented is correct in this respect.