Sorry if I missed it (or didn't get back to you), I'm trying to (and failing miserably at)answering whatever questions I can.Still waiting on him to answer my question, but I appreciate all the info all the same.
I haven't taken the clamshell off yet but after staring at it for a day it looks like the warping / waving of the horizontal ledge around the mount points might actually be on purpose to avoid further stress around the bolts. The material there is definitely pliable enough. The design of the seals elsewhere on the roof gives me confidence that it's right here, too. The seating pins and slots make it impossible to install the roof in the wrong position or misaligned.Thanks for all the info. Would be interesting to get your opinion on hardtop removal, and also how the hardtop mates with the body. The wide hardtop flange makes it difficult to visualize how the two are mating up.
The slight warping of the flange you mentioned (the longest section between two bolts on each side), is something I saw as well when viewing at a dealership. Although it didn't seem enough to cause a sealing issue.