I worried about this when I got a new set of rims and TPMS for my winter tires. I asked the smart tech about it when I had it in for service, since I planned on storing the other set in the garage where my car lives. Here's the story I was told, which seems to match the explanation in the service manual:
The SAM remembers the last 4 TPMS serial numbers it saw and expects those. When the tech puts the new tires on the car, they generally reset the SAM. It's not required, but it forces the system to start up in re-train mode. (This can also happen if you've disconnected the battery for more than 20 minutes.) When service is done, they take it out for a spin and then to be safe they hold the cockpit button down for 10 seconds, even if the light doesn't come on. They then usually drive it around for another 2 or 3 minutes to make sure the light doesn't come back on (eg that it got the right sensors).
It's important to note that this can be done at any time, and doesn't explicitly require a dealer visit. You can force a re-train any time by holding down the cockpit button for 10 seconds. So if in doubt, find a country road and hold the button down for a bit.
