There's going to be no savings by not heating or cooling certain parts day and night like that and will end up costing more in the long run having to install the more complicated system now and whenever it needs maintenance.
No savings may be a bit too strong .... it really depends on the layout -- but, even my row in the city w/ three floors was over 1100sf. So I'm guessing not that 3 floor layout -- we did save something not maintaining full temp on all the levels. But -- you are correct it's not really for cost at that sf size
The zoning equipment is not all that expensive as an add on. The better carrier equipment (infinity control) is all set up for the zoning control board to be added (The main Thermostat is the same) The actual zone valves are not at all expensive. My last was about $1600 for all the extra equipment -- 3 zones and 5 valves.
Also -- I have never had any parts fail out of warranty. We lost a board on the first one we did at about 8 years in 2011 and I had an early damper start to make some noise on one installed about 6 years ago. No longer own the first -- sold it to a friend.
Most of the equipment is actually robust ..... Carrier has a 10 year parts warranty. Even if a board fails after -- at that point there is e-bay.
It's like my built-in refrigerator at one place. At about 10 years + or so you can pick up the $450 boards on e-bay for pennies. After a few years when they no longer make them they get expensive or impossible to get. I have spares of a few parts because I have to fix my unit as it's in the city and they no longer make that size. My plan is to paint the kitchen when I move ... not replace it for the want of a refrigerator.