So I've noticed something about the flow of the BTC refunds that did show up, which makes me think that the funds were never in fact converted to USD.
This is irrelevant. The price of the product (to buyers, and on the material end) is USD. If Tom or BTCFPGA decided to take the risk of keeping the income in Bitcoin, that risk - and any potential gains/losses - is his.
To me, the issue is really that if he didn't convert the BTC to USD, how were the ASIC R&D funded? Tom collects BTC and then pays for the chips development out of his own USD profits from the MMQ? Seems unlikely, as that can bet pretty expensive I would imagine.