Just to close the loop on this one, here's what I ended up doing:
I just cut through the little strip of the windshield skirt, right in the center.
Then all I had to do was file a tiny amount of material off of each side (like less than 1/32" I'd say), until the two sides could sit flat next to each other, then I riveted each side to the firewall flange.
That's it! The little seam is not perfect, but it's a lot less noticeable than that giant bulge was.