Nice link! From what it describes, I don't think this will be too much of a problem for a tracking system like this. The randomized MAC is only changed when the phone is put to sleep for at least 120 seconds. It stays constant while sleeping, or while active. So if you're on your phone from start to finish (as a lot of people do) or if you leave it in your pocket from start to finish, you'll be tracked fine. Only if you use your phone, put it to sleep, and leave it asleep for at least two minutes all while in the line will you defeat this. And while that's certainly something people will do, plenty of people won't, so the tracking can use those.
This all sounds pretty good to me. Short-term tracking like this is useful and not very invasive. The randomization will still defeat long-term invasive tracking, like a store recognizing you from past visits and building up a database of your individual activity from that.