The reason that EW are on the hook because if its established the Passenger Rights Regulation is enforceable, as it was here, the claim is against the carrier, not the agency because that's how the Regulation is constructed. The claim was brought under 261/2004 rather than the contract. I like Dr. Böse's cases for the claims he brings under the BGB than the Regulation.
For example, if pax are entitled to a refund due to irreg, that's to be paid within 7 days, whether that's via the agency or the airline, it's 7 days. And if the airline sends the money to the agency and its "lost" or "stuck" like during Corona, the pax's claim is still against the carrier not the agency and the carrier ends up paying twice- tough luck. It's not a contract law issue but by way of the irregularity situation there's a direct enforceable obligation between the pax and the carrier that is otherwise not there.
In terms of the CJEU adding further rights to the Regulation, that's nothing special, the CJEU is a political court that seeks to expand the scope of EU Law, that obviously goes all the way back to Van Gend en Loos. A lot of EU law is really poorly drafted, some scholars consider that to be deliberate.