Biometrics instead of passport stamps is getting more common at international borders. I'm not surprised the EU is doing it, although I am surprised it took this long. The article says that this system has been delayed for a while, so maybe that's why they are behind the power curve.
I know we use biometrics at airports. My last visit to the UK they were using photos and facial recognition at entry. Several Asian countries use fingerprints. I want to say when I flew into UAE and Kuwait commercial both of them had a biometrics system, although I was on an official passport and skipped it. South Africa had fingerprint scanners when I went this summer, but they weren't using them the day I went through their passport control (FWIW, there were huge signs in the Johannesburg Airport saying SA was upgrading their entire entry control system this winter. Their version of Real ID, I guess).
Long Story Short: Biometric Passport control is common, and growing more so, the EU getting on board isn't a big deal.