If 9to5Mac were run by reputable journalists, this poorly-researched article with its conspiratorial conjectures would have been taken down already.

The explanation for the Apple Pay aspect is something called the Payment Account Reference (PAR). Mastercard has a brief overview. Everything is working exactly like it is designed and as advertised. Apple Pay is not (and cannot) send your full real card number, but if you give a merchant your real card number, they can look up a reference number shared by every token associated with the card.