Fair point. Pucatrade is essentially a virtual binder of cards you say you have. You can easily lie about that. Centralizing the cards allows for the creation of a token that is transferable between users. If someone trades you one token, you know that it's not with the person who gave it to you, it's with mtgex.

Pucatrade also created their own currency which they themselves have complete non transparent control over. They can print as much of it as they want at any time with no one knowing about it.

Even though it is centralized, a blockchain / smart contract based solution offers transparency. Along with third party audits of the physical cards users can have some measure of trust that the token they hold correlates to a real card.