Either you have motor controlled dampers, which means the system can't be entirely responsive all the time, or everything is open all the time, which means you are losing a lot of airflow to parts you don't need them.

It is motor controlled. It has two thermostats and it adjusts the motors to only heat or cool one floor.

I'm not seeing why that wouldn't be equivalent to two units.

Okay:

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)