I have a separate set of Winter wheels which obviously come with their own pressure sensors - so my licence plate/tyre sensor ID pairing will change at least twice a year(I also got a flat once and put a single winter wheel on - what happens then? surely you will get 2 different IDs for one car?).

That's a fair expectation and can be filtered out: you can roughly expect 1 plate to match multiple set of tires. When the same set of tires (or 3 or them) get matched to a different license plate, that can be flagged as suspicious.