Extending the side raels up a bit?
For a different reason but I made my outside skirt cover about 1/4" higher than stock..In other words it does not line up with the top edge of the rear skin behind the roll bar...I thought it looked terrible, but no one ever notices it..Not even me..
Now I'm thinking that maybe you could also add an extension flange on the inside that is rivetted to the existing inner rail..The rivets would be between the screws.
That way you could position the screws so the edge distance is correct on the plexi..But don't worry about it on the inner flange.
It will look the same as mine...I.e just fine when you stop looking at it...
I could probably find a pic of mine if your not convinced.
Frank