The thrust of that paper is that using special equipment it's possible to use a genuine stolen card to do a non-PIN transaction, and that banks will often claim that PIN was used in a card-present transaction in order to avoid refunding money.

In the UK at least, and with a credit card, the bank is legally bound to return the money pending investigation, regardless of the circumstance.

(I agree this doesn't help with the BTC situation because chargeback is still a possibility)