Hey Iggie, it's actually whatever uses the LEAST points that determines it, when you are going to a "zone boundary" city. For example, if you are going from Chicago to Denver, it's one zone. If you are going from Seattle to Denver via Sacramento, it's one zone.
And you can use zone cities to your advantage on longer trips. For example, I am scheming up my next AGR awards trip to try and get from coast to coast (a three-zone trip) via certain routes I have not taken before, like the Cardinal. If the routing via Cardinal is not shown on a simple point-to-point trip, I can force the routing by going from the west cast to Cincinnatti ( a zone boundary city on the Cardinal's route), and then from there to my destination. That would be West Coast to CIN = 2 zones (20,000 points in a roomette), and CIN to east coast = 1 zone (15,000 points in a roomette). 20,000 + 15,000 = 35,000 (same as just doing the three-zone on a point-to-point award). How cool is that? I hope they are not thinking of changing it...