Overheating of the 2nd floor/Over-cooling the 1st floor is a valid concern with a zoned or 2 separate systems. The systems could be designed to "swap returns", the upstairs system gets it's return air from downstairs and downstairs gets return from upstairs. With the "swapped returns" it may be possible not to have ANY A/C required for the downstairs IF the returns were strategically located. The same could hold true for the upstairs, getting all of it's heat from downstairs.
The issue with "swapping returns" is in summer you want the return at the hottest point which is in the ceiling of the top floor and in winter you want to pull the cold air near the floor of the downstairs.