I think cutting the bottom down would be major surgery requiring so much re-welding that it might defeat the purpose. Would mean re-installing the frame pieces at the bottom all the way around, plus whatever gasket material is there and mounting hardware, etc. If you have the capability for that, it would probably make more sense to just fabricate an aluminum cover yourself.
(I still struggle to see how the advantages of caps outweigh the disadvantages. Two use-case scenarios came up recently with my Santa Cruz are moving a stove upright in the bed, and handbombing a half pallet of bag mix concrete. The first would have been impossible without laying the stove on its side and risking scratches/damage, the second would have been a much bigger PITA without being able to stand in the bed to load/unload. For taller loads than the tonneau, I have a waterproof canvas tarp and bungee net tucked into a bed compartment in case it rains. Or what
@GreyGhost said before I finished typing...)