I'm not sure how close your cap wall is to my GMC 6500, but when I did mine I left the upper curve of the the rear window frame, and cut straight down on both sides, then across right at floor level. Then a sheet of steel with a matching cutout became the front wall of the new box, which got bolted all the way around the sides and top, and welded with a piece of angle iron covering the bottom joint. Ended up very rigid, no weird flexes or creaks driving, and no boot to leak, just a nice bead of auto body seam sealer around the outside.
I know your situation is different as you have to use a boot, but I guess the point is don't be afraid to cut a big hole, every factory conversion has one, no big deal. Me being in the habit of maybe overthinking things, I'd probably agree with your mechanics that you'd want to reinforce the edge of the cut sheet metal to keep it stiff. Maybe a framework of small square tubing? Set back from the edge enough to allow the boot to slip onto the sheet metal edge. Of course I don't know what is available for boots, there might be something that is big enough to slip over say 1/2" square tubing, just bend the tubing in the shape of your opening and weld it in place. Just brainstorming as I type.
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