The corners are turned up so when you fold the wings they don't get caught. They might be up more than they need to be.
For my rear covers, I got foam that was about 3/8" by 3/8" but I could squish it down to almost nothing. I thought it was a little too thick but after I put it on I think it's just right as it fills the gap on the curved parts. I just went to an industrial supply place similar to Acklands and looked at automotive weather stripping.
I never put holes over my bolts. I just figured if I ever need to take the wings off, I can unbolt the top of the sky light enough to get at it. It would be pretty easy to make covers.