Probably because you then need pillars throughout the entire building to support the second floor which you are loading down with a ton of weight. The average forklift weighs 3x or more the weight of the average car, and then adding racking and stock on top of that. Yeah if you completely redesign your storage system to not require forklifts you save weight there, but you end up adding the weight back with all the heavy duty track systems and extra heavy duty racks that are required to eliminate the forklifts. Plus there is liability of having that weight up top, a rack failure on a second floor could take down half the building.

It is possible, but you end up spending 10x as much on the building.

Then put the warehouse on the first floor and put the store on top.

Lots of big cities have grocery stores with parking garages under them, doesn’t seem much different.

I think this is correct. A lot of these buildings seem to be post frame or poll barn style. Relatively cheap for building large square footage buildings but add some limitations to multiple floors. Even if you put the storage floor under the shopping floor you'll run into tons of issues with buildings of these sizes that don't have a ton of pillars for additional support. I mostly see these stores built on vacant "rural" land on the outskirts of cities rather than in city centers themselves. Which means the single floor square footage is rarely an issue and not something worth designing a building around. If you have all the space you need to go wide, it's almost never worth going tall.