Presumably EASA, Airbus and the very small number of affected airlines have been talking about this for a little while, and EASA is satisfied that the checks Qantas did during scheduled maintenance, while the directive was being drafted and finalised, fully comply with the directive.
After all, the requirement is for prescribed checks to be undertaken before a particular date. Qantas and Airbus have under taken those checks, before that date. It'd be pointless for EASA to require them to undertake those same checks again.
The article says what it says. Figuring out how it likely happened isn't that hard, really...