If you need to be already logged in the device that reads the QR code, then the QR is no longer encoding a magic link. It is more similar to doing the 2nd part

If you need to be already logged in the device that reads the QR code, then the QR is no longer encoding a magic link. It is more similar to doing the 2nd part of 2FA (after skipping the 1st) but adding unnecessary complexity in between. If we expect the user to be already logged in on a device that they have at hand, why give them a QR code instead of simply a PIN code or a notification to confirm the new login?