Just to report, I pre-filled out VJW a week ago, but still filled out the paper disembarkation cards. In line for immigration at Narita they ask you to show either or, but not both. The line gatekeeper has a paper asking to show either the paper cards or the VJW QR code to enter the line. No need to do paper cards anymore.

To add, at customs you can use the second QR code at the automated gate, scan your paper, QR code and it takes a photo, then you go through customs with no inspection if you have nothing to declare.