>intercepting traffic or spoofing a site can copy/tamper/replace the QR code

Will this be a problem with HTTPS?

When you open a page, a request will be made to my server to generate a unique login attempt, the id of this unique login attempt will be shown in the QR code. When you scan it and enter your phone's pin, my authenticator generates a signature of the login attempt id, your username on that website and the current time. My server verifies the signature and logs you in if everything is ok.

Have you logged in to the Discord/Reddit/Whatsapp websites by scanning the QR code shown there from their mobile app? My concept is the same but using my authenticator app, websites which do not have a native app can also offer a QR code login.