@KroalerThanks for the information! Most of what you said is a better articulated version of my concerns.
Based on my amateur understanding of HVAC, I do believe our system is properly sized. With the exception of the upstairs in the summer, the house heats/cools evenly and the system doesn't cycle on/off too frequently. I'll fiddle around with the calculator, but a lot of the insulation ratings are just guesses. A few factoids that might be relevant:
1. The hot upstairs issue is universal in my neighborhood in Denver. I think it's the newer home design with a lot of attic insulation that
mostly improves home performance, but has a tendency to trap heat upstairs. It's a common theme in neighborhood facebook groups and summer gatherings. We can usually solve this with open windows and ceiling fans unless the air quality is bad, or a true heat wave where it stays hot at night (1-2 weeks per summer). Since we mostly use open windows and fans upstairs anyways, I don't believe that zoning will do much for this problem. Although the whole house fan might. I am buying an air quality monitor to help understand when open windows are a good or bad idea.
2. The HVAC system was actually designed and ducted for zones. There is separate ductwork for each floor, and wiring for thermostats. They just never installed the louvers or the controllers. A neighbor had their system with the same setup zoned (built by the same builders at the same time), and they claim their electric bill went down by ~10% in the summer, but not much impact on the winter. They're naturally more aggressive about using the AC than we are though.
3. As a general rule, houses in my neighborhood are well designed and speced, but were built by drunken monkeys. I have general confidence that the system was sized correctly, but wouldn't be surprised if it was installed poorly.
4. I'm in Denver, so basement humidity is never an issue. I have more of an issue with dry air.
Edit to clarify: I don't think that zoning will do much for the top floor, and I wouldn't run the AC more to cool the top floor. I'd mostly use zoning to shut off the HVAC to the basement. The real question is the one you brought up, which is whether this will just make the ductwork less efficient, or whether it will actually move more air through the rest of the house.