Hi Giovanni,
You are welcome!
I am not sure if the visualization artifact has been fixed or not. I can check and let you know. Are you seeing any discrepancy between the index result and the geometry you have set? I think the issue was that the indices in the top layer and bottom layer were extending into the substarte and superstrate. Even if you do see this, as you said, this shouldn't affect the simulation results. I remember the Development team had told me that the right way to visualize the index in RCWA is to look at the index of each transverse layer (instead of looking along the propagation direction), but I do think that this might not be insightful sometimes.Â
You can use the absolute postions as well. The advantage of the "reference positions" is that if you change the height of any of your layers, either manually or using sweep, the RCWA layer positions will automatically update. But in absolute position, it won't get updated. So, if you are planning to change the height of the grating or any other layer, then the reference positions would be the better choice, otherwise the absolute positions should work as well.
Regards,
Amrita