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.
True. I'm just pointing out that they appear to never have been converted, contrary to some opinions.
I know this is based on some conjecture, but I think the evidence looks highly suspicious. I think it's quite likely that those 500 BTC were from customer funds, or that he had everything mixed together (inappropriately).
I think it is highly likely he had everything mixed together - but why is this automatically assumed to be inappropriate? MtGox certainly stores all the user balances together, and bitcoind does so even if you have separate accounts setup. Perhaps ideally, things might be different, but that doesn't change the reality or realistic expectations.
I dunno, I don't think it's too appropriate to keep business and personal funds mixed together in the same account in these kind of large amounts. Maybe you disagree.
I concede that I'm guilty of the same when it comes to my tiny USD-based business. But I don't hold massive amounts of pre-order funds. The risk is all mine.