Their liability figure for all we know could just the actual dollar/yen withdrawals it wants to make good on, and dollar/yen deposits it plans to refund - taking into no account internal customer btc/fiat balances.
Yes, that would be the most logical approach, methinks.
Suppose the client deposited 50 BTC when the price was 10$, and by trading inside MtGOX he managed to have 1000 BTC and 2000$ in his account at closing time, having withdrawn 30$ at some point. Methinks that he entitled to get back only the 50 x 10$ - 30$ = 470$ that he put in, not the 1000 x 500$ + 2000$ = 502,000$ that he thought he had. Makes sense?
EDIT: However, courts use a "logic" that is quite different from the usual sense of the word.