The EU Payment Service directive does not distinguish between domestic transfers and SEPA payments, as far as I can see. Opening an account in another country doesn't help either. The bank will probably allow it, but it will be illegal for MtGox to transfer more money to and from customers without a license, and breaking this law would be very unwise when they are applying for a license. It applies to all money transfers within the EU. Do domestic PLN transfers and SEPA transfers originate from different accounts, btw? Some banks allow multiple currencies in the same account.
They come from different account numbers (but have the same bank/branch identifier, of course).
Domestic PLN withdrawals have currently even longer delays than SEPA, though.
Still, they might be in the same queue and experience some additional problems (like lack of PLN in stock, for example).