Disclaimer: Kraken is only assisting the MtGox trustee and doesn't speak for the trustee, so nothing I say here can be understood as a promise or guarantee about how the claims process will actually work.
So if I understand it correctly ALL currencies are converted into JPY with a conversion rate from the date that MtGox went offline.
For the purposes of the claim form, conversion rates from the day before the start of bankruptcy proceedings are being used to determine how much you are claiming in JPY. For BTC, the the conversion rate is 50,058.12 JPY (equivalent to $483 USD at the time). But keep in mind that these conversion rates are only used to determine the value of your claim in JPY, and do not indicate the actual rates at which currencies are or will be converted.
After the deadline for the Bankrupty Claims and after checking all the claims, the trustee calculates a percentage, based on the total available JPY and the total amount of all approved claims.
At an unkown date the trustee will payout the percentage based amount to all affected customers. This amount is in JPY also. If you want to be paid in a different currency, the amount of JPY is converted into that currency with the conversion rate FROM THAT MOMENT (the payout date).
Example
If I would like to be paid out in Bitcoin, an initial conversion rate of $483 is used (correct me if I'm wrong).
Let's say I've 25 Bitcoin and the calculated percentage will be 20%.
Total claim value in dollars: $483 * 25 BTC = $12.075
Payout 20% = $2.415
Conversion into Bitcoin based on initial rate ($483) = 5 BTC
Conversion into Bitcoin based on current rate ($230) = 10.5 BTC
So far as I know, the trustee hasn't explained how the payout calculations will go, but I think your example is a likely scenario. However, presumably the payout in BTC would be based on the current rate and not the $483 rate. So the payout in your scenario would more likely be the 10.5 BTC amount.
In the future the trustee will ask us again in what curreny we would like to be paid out.
If the above example is correct, the final choice from everyone will depend alot on the Bitcoin conversion price (September 2015?).
If the (near future) Bitcoin price is to high then there is a risk that the trustee has to sell Bitcoins (market/auction)...
Another thing is that if the Bitcoin price will be $800 at the payout date, the trustee will have Bitcoins left in his wallet AFTER all the payouts are done.
On the other hand, if the Bitcoin price stays at the current rate, the trustee hasn't enough Bitcoins in his wallet to payout everyone.
Presumably the full remaining value of the MtGox estate will be distributed with each creditor getting their share. The bitcoin price used for the distribution just determines what the remaining value of the estate is (measured in fiat). So everyone who files a legitimate claim should get paid and there shouldn't be bitcoin or any other funds left over (except maybe if there are remaining expenses that will need to be paid). It might turn out, though, that the trustee can't accommodate everyone's preference for BTC or fiat payout without buying or selling some bitcoins.
Arguably the best choice for creditors is a BTC payout regardless of price. The reason is that the majority of the MtGox estate is in the form of bitcoin (around 75% at current price), so creditors have an interest in supporting BTC price. If not enough creditors ask for a BTC payout, the trustee may decide to just liquidate all the bitcoins, either by auction or on the open market. Selling such a large block of coins is very likely to have a significant negative impact on price and therefore a negative impact on the remaining value of the MtGox estate. If anything, it would be better for supporting the value of the estate if so many creditors asked for a BTC payout that the trustee felt pressure to liquidate the fiat by converting it to BTC for payout. I'm sure some creditors have good reason to prefer a fiat payout, but they should keep in mind that a request to get paid in fiat is essentially a request to have the trustee liquidate their bitcoins and this may have a significant negative impact on the return value they get.