It's somewhat simpler than that. QR codes use error-correcting codes in order to deal with things like damaged codes, etc. The QR code reader treats the logo or art part of Paperlinks' codes as damage, and uses the error-correcting code to fill in the blanks. I did the same thing (only less artistic) with Groovebud's codes.
https://chrome.google.com/webstore/detail/agpbffgdfhnhloelam...