Most garage floors are not really flat. At least mines not. I feel that using the fixed points of the damper are better for a home setup than the ground clearance as it has a lot of stacking tolerances. Ground should be checked to make sure it's in the range you want. I personally had all kinds of trouble adjusting without scales using ground or fender clearance.
My shop floor isn't flat either, but it can be shimmed to be level. But, that doesn't usually become an issue until you're aligning the car. Not so much of a big deal for setting the ride height since we're trying to get it close and not perfect. I think we might be saying the same thing though. The measurements I took were battery pack to floor for clearance, then axle nut to fender for ride height. I know there's some variance in the plastic fender trim, but it was good enough for me. I wish the Hubstands would work with these cars. Would make a lot of this process much easier