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.
Agreed. When you make a purchase denominated in US dollars, it is the equivalent of selling your bitcoins for USD on the spot and then paying those dollars to the vendor. Unlike what some people on these forums believe, the price of BTC is not guaranteed to go up. Imagine the shitstorm that would occur if BTC had fallen against the dollar and then Tom refunded people their exact BTC payments.
made it perfectly clear that when we placed our order it would be as if we were selling our BTC for USD at the price that the order was placed.