Are you looking to get rid of the seam altogether, or just the weather stripping? If just the stripping, you could likely use body panel adhesive or windshield sealant, smooth it out before it hardens, then paint it.
An Xterra style rack would help with the lines, so would an exo-cage, if a cage is in your long term plans.
I believe this was done by Marlin's shop 10-15yrs ago.
I actually thought about copying this truck and chopping off my bed. I ended up cutting 14 inches out of the bed instead. The gas tank and modifying the frame was the items that helped me decide to do the bob instead. Anyway will body panel adhesive hold up to the flex between the the fiberglass and metal? Would I need to bondo the seam after joining with the adhesive or use something else? Exo is in the plan but it is going to have to be after paint.
Thanks for the ideas