Pictures as promised!
The first two are the underside flap I was speaking of. Basically a triangular piece to somewhat match the tent side, seal to the truck and seal to the tailgate. First pic is it hanging so you get an idea of it. Second is kinda tough to visualize yet it's in place under the tailgate (tailgate end at the bottom/truck at the top. left side if that helps).

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Still a bit wrinkled, yet hey, first time ever doing something like this..

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Next pic is what I was speaking of to roll the bottom inside so we can seal it once in the topper.

And of course how long it is before being rolled in. This allows me to seal it once outside and still don't want those little buggies to get in.

One thing to notice in this repeated pic. It's the bottom and the fold/lap. This helps shed water and not let it inside. I probably should do the same to the bottom of the entry panel. To be honest, I was scared to and screw it up.. again..

Yet now that I see it and am a bit more comfortable about doing it, I will.

Builders note: I never even thought of these lapped seams till I hit the point of the zippers and shedding rain away from. First, I would have made the sides longer to wrap more on the backside allowing for better protection. Next is I would have done it also at the top of the hatch/entry. I did work my hems in the though of rolling water off, yet a lapped seam would have been much better.
Would I have gone for a fully removable hatch cover? I still say no, yet you may find it fits 'your' requirements. Pro side would be remove and zip in a screen. Con side you loose the option of a fly if extended. I lean towards another zipper and make that one full to add a screen. That wouldn't be easy dealing with all this material..
Next of course is choice of material. I would have gone with ripstop nylon if I had found enough at the right price.