[elhigh]

Here's my last input on this:
I would go with the Lexan. I have a window I made from Lexan here at work, and I often approach it from far down the hall - I can see very clearly through the window even as far as 75deg from perpendicular, BUT that window is cleaned every day. So your mileage may definitely vary.

THAT SAID, go your own way. It's your ride; if you want flaps, then by all means go for the flaps. Lord knows, if you can make it so you can reach in through them to fetch something out of the bed, without having to completely open the cap, then that's not a complication, that's a convenience feature. I can't tell you how many times I've wanted something out of my truck's bed, but it's more than arm's reach from the pass-thru, and more than arm's reach from the tailgate. And if the flaps are body color, then out of sight is out of mind, right? Less temptation for some mouthbreather to try to make an unauthorized withdrawal from your tool collection.

Vaya con Dios!