Thanks Mike for the explanation of how the clear part has raised bezel rings. The clear part then sits on top of the decal which I assume is attached to some kind of backing board.
The problem you have is that the clear part is too thick, and this is made worse by the raised bezels….correct?
Your fall back position would be to leave out the clear part from the build completely. But I would have a shot at modifying the system to make it work better.
If I had this problem, I think the best option would be to sand the clear part from the back leaving the bezels intact. The bezels in photographs look quite good, but I can imagine that they stick out too high with the plastic so thick. If the bezels themselves are too pronounced, you could try sanding the piece on the bezel side, making the bezels less pronounced in that process.
Before you do anything, I would make a copy of the IP Decal and perhaps also make a stencil of the clear part onto clear plastic like what you see in some packaging. If you make copies and a facsimile stencil you have the ability to redo if things head south at least