So, the answer obviously is: the Guardian got the font far cheaper by allowing it to be sold to other customers, and (relevant here) not paying for a license that allows sub-licensing (which would be completely useless to them, anyway).
I wouldn't be surprised if it was actually a deal where no money changed hands, with the foundry getting the Guardian name for PR, and constant feedback during the design process.
As to web design: unless otherwise specified, web design is covered by the same copyright rules as fonts (or movies, or books,...). The correct analogy actually is a customer selling your design to some third party, something that probably would upset quite a few designers.
As for the customer changing a design: that's an infringement of the creator's so-called "moral rights". Its legality varies between jurisdictions, I believe.