RE: rear window seal
I would not put a rigid filler(aka Bondo) in the gap. When setting windshields, a common mistake is having a corner or side touching the steel opening. This will most surely result in a cracked windshield at a later date. The expansion rate of the glass vs. steel is such that the glass will expand with enough pressure to stress the glass so as to cause a break. I would think the same holds true for the rear glass.
FWIW, I have heard of trimming the seal back as it is not actually a seal per se. I haven't seen one(or a pic), so I'm not sure what it would look like. But done properly it should look a lot better than the lasagna. Any gap could be filled with black windshield silicone. Fortunately, my '93 has only 3 ripples. All on the upper passenger corner, two on the vertical and one on the horizontal trim.