I doubt that. $99 is probably just above cost with 1 controller, depending on production volume and how you factor in NRE. Generally speaking the big price break on electronics comes at 10,000 units which I imagine would be on the low end of their intended order given the number of backers already.
Most of the cost in mobile devices lies in the screen, battery, touch panel and associated circuitry. This device doesn't have any of those. A Tegra 3 SoC only runs about $15 in volume. For comparison, Apple sells the ATV for ~$100 and the original was reported to cost ~$64 to build, I don't have any data on the newer models but I doubt the cost has changed much, if anything its lower.