Nigel.
I appreciate your point and is why I stress the importance of yield. But were you informed of the upgrade in advance or did it only happen at the gate? My experience suggests upgrades are more likely to happen with frequent flyers and the like, especially when economy is full, and is carried out at the gate when original boarding passes are switched. When that happens, I'm not sure the seat plan the day before would take that into account.
The seat plan this morning for the JFK which showed economy full and only 6 seats taken in Business could well have resulted in a few upgrades later at the gate, but I hope they hadn't already been reflected in the 6! But yes, not all will have paid the full price and maybe even staff have been allocated J class seats - does that happen?