If I understood it well, with this tool you can change secret AES key, but you need one from Yubiko in case if you want to be authenticated by on-line services. Yubiko's keys are stored in the moment of creation. If mtgox overrides it then you do not have the valid key 
If I understood it well, if you blow away your AES key on your Yubikey, then you'd have to convince MtGox to let you update the AES key on their site before you could keep using it with them. Chances are they're not going to want to do that - they'd rather just charge you $30 and send you another key.