Our windows are fixed in much the same way. I opted for the foam tape. My windows fit flush once clamped onto the seal, I used 3mm thick seal (6mm polycarbonate windows). I was a bit dubious because the width of the seal surface is only 10mm but we have had no problem so far. Certainly beats the gooey stuff!!
-------------------- The pessimist complains about the WIND: The optimist expects it to CHANGE: The realist adjusts the SAIL