"Isn't there always a material interface in the simulation as long as you have materials / structures? Could you provide an example of what you meant by this?"
not true. When the substrate is truncated by PML, except the top air/material interface, there is no other interface.
Since it is a cavity, and you plot transmission and reflection, it is normal to have different peaks and valleys. PLease place a monitor behind the source and add R+T to check if it is smaller than or equal to 1 within simulation errors.