You are absolutely correct. You end-up running a huge compressor for a small zone.
I've always like the idea of chiller systems and the general concept of storing what you need during times of high efficiency to bend the curve in your direction.
I haven't done any math on this at all but I've wondered what it might be like to cool the massive foundation slab most homes have as well as the ground directly underneath them during the night. Again, I haven't thought this through at all. Just thinking now that you would want to treat the soil in order to have a stab at improving heat capacity, etc. You could then use that during the day in a very careful way to compensate for heat flow. I almost envision radiator panels embedded into the walls with sensors to pump heat into the cold ground only as needed. Anyhow, there's probably a million things wrong with that idea. Air conditioning is one of these things that could be so much better.
I'm not seeing why that wouldn't be equivalent to two units.
Two small units
For the sake of argument, let's make everything otherwise equivalent. We'll say the small units are 1.5kw each
When upstairs and downstairs call for heat, you use ... 3kw When upstairs calls for heat alone, you use 1.5kw When downstairs calls for heat alone, you use 1.5kw
Ducting/blower loss from this setup (assumes two completely separate duct runs): 0%
One large unit:
3.0kw to make life easy (in reality, if you use small units, you often need less)
When upstairs and downstairs call for heat, you use ... 3kw When upstairs calls for heat alone, you use 3kw When downstairs calls for heat alone, you use 3kw
Ducting loss from this setup: 25-30% (at least, it's just the way it goes due to longer duct runs, more tees, etc. If you have, say, flex runs, it'd be even more)
It is essentially guaranteed to run for more than half the time of the smaller units (due to ducting loss, etc), making overall cost more.
Note that if you had mini-splits as the small units, the comparison would be crazily in favor of that. you'd have no loss due to ducting, they would almost certainly be DC based, and would be completely variable to actual load (even a "variable speed blower" on a large unit isn't), not 1.5kw on/off. Smaller unit efficiency is also almost always greater than larger unit efficiency.
Also note this is all a comparison of efficiency. It may be more cost effective to do one or the other (though it depends how long you own the house, insulation, blah blah blah)
It's simply not efficient, even with auto-closing dampers, to zone and duct a multi-zone system with single condensing units.
You'd be much better off, efficiency wise, either: 1. Using mini-splits everywhere. 2. Going geothermal. You can support multiple units off a single loop. I did this in maryland. My 4000 square foot house had all the hot water and cooling provided by GSHP. My energy bills, keeping it whatever temperature I liked, dropped from about 400 a month in the winter to about 50 bucks. The wonder of 41 EER, 5 COP. Unlike the air source heat pumps, they actually publish real efficiency curves for various temperatures, and your pump actually work at close to expected efficiency!