Not to mention MM has probably hit the bank smiling already, because SHIPPED is what matters to them, and retailers bought lots of copies, and with a studio as small as theirs, I'm sure it was good for them.
I don't know anything about the particular agreement between Media Molecule and Sony, but in general, developers care about sold, not shipped - each quarter the publisher pays royalties based on what's shipped last quarter, minus what's returned from retail the quarter before that.