I've considered making my own flush-mount tonneau since my snapless roll-up is getting worn and sticks about 1.5" above the rails. My concerns that have prevented me from doing so were rigidity of the panel (I like the aluminum rails on the sides and the cross-rails every 16" or so to support the vinyl).
The key thing I've found is: a single 4x8 sheet of plywood will NOT cover a full-size truck bed.
Inside bed width is more like 60+ inches. The 48 inch bed width is the width of the bedfloor between the wheelwells. The open bed is quite a bit wider than that. This would require using two separate sheets turned sideways so it's not insurmountable, but adds to my concerns about panel rigidity.
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