While I can't comment on the electronics and warranty bit, but to me I would think it's just a feasibility issue of the current design more than anything.
Case in point are the two high level brake lights. My guess is that the tonneau would have to cover the whole of the rear of the folded top which would block the lights. Perhaps plastic inserts could be sewn in but I'd image there would be some alignment issues and maybe even legal issues in covering brake lights.
If someone were to make a cover like had cutouts for the lights, I'm not sure I'd want one as it would let water in which defeats the whole purpose.
Just a thought.
