Amiga is a bit more complex than a C64 in a joystick... Im sure the higher costs involved reflect alot of R&D time, etc...
Jeri had already done alot of the work for the C-One before the DTV. So most of the R&D time had already been paid for or written off. It probably wouldn't have happened if they'd had to pay her for all her time up front.
The C64 was a much better known computer than the Amiga, so the cost of hardening the design into an ASIC and mass production was worth it. I don't think we'll see the situation repeated.