The rates on their website only applies to online orders, for which they charge 500 yen for delivery fee, no service fee involved; however, typically you have to pay fee when transfer money at the ATM so that's extra. I don't know about at shops. I couldn't find anything about the service fee on their website.

The rates at their shops can differ from the online ones, as big red letter says "下記レートは通信販売限定のレートとなります。店頭での両替レートとは異なりますので、直接各店舗までお 問い合わせください。", use it as a reference but not as an absolute.

BTW, since you are from SFO, you are traveling there over the Thanksgiving holidays? Because me too! LOL