But then you might want to use it with lets say glossy plain-coloured melamine sheets - most surface trackers have a lot of problems with this, so the calibration stickers are a cheap and reliable solution.

The only issue I can see is kick-back from the router bit, especially if you use larger diameter bits - this can throw the router significantly, and unless the control system compensates quickly yet gently, you may well lose tracking, leading to undefined results.

I wonder how a optical mouse sensor would react to the vibrations of the router.

With optical mouse type tracking wouldn't you lose your position relative to other cuts if you lifted the router off the workpiece?

I imagine you can integrate information from a QR-code for global positioning and an optical mouse sensor for fine tuning