Because Mt. Gox is a corporation organized under the laws of Japan. Corporations in Japan can own many things of value, such as hotels, laser printers, intellectual property rights, Alpha Black lotuses, swiss francs, and promises to be paid in the future... but all of these things exist, on their books, with a yen value next to them.

In the event of a bankruptcy or civil rehabilitation (民事再生, which is what Gox is going through IIRC), creditors generally get paid out in yen, not in cement mix, even if the company only happens to own cement mix.

I'm sure that the creditors would love to be paid back the full XBT amount that they lost, but since it's a legal proceeding they essentially have to operate in the currency of the realm which, given that Mt. Gox was a Japanese company, is JPY.

Because currency describes the value.

It's like MtGox was an apple storage facility and lost all your apples - you wouldn't get apples back, you'd get the value of those apples.

Which is in a real currency.

Because when debt hits the legal system, as is the case with bankruptcies, it gets converted to the currency in which the legal system works.