What exactly are you suggesting the QR code is doing? My phone shows me the URL encoded by the QR code before opening, and I've never seen one with any additional information in the URL. They're not dynamically generating QR codes for you...
Using your device to read the menu puts your device in the loop where formerly it was not.
It's not comparing websites accessed via QR against every other already tracked thing in society, it's comparing it with laminated pieces of paper.
I didn't mean they generate QR codes dynamically. It wouldn't be hard at all to encode the table number, for example, and then of course they have the time and know your reservation, and thus can identify their customer's phone.