Put the entire building over 'em. And solar panels over the building. The Target near my house is built on top of its parking lot. I don't have to cross an entire parking lot, dodging traffic, when I go there by bike or on foot. And it's on a bus line. What's not to like?

The exepense is what's not to like. Far cheaper to build a single-story warehouse + outside parking lot than a second story above a parking garage.

In most places in the US, land is cheap enough that paved surface parking is cheaper than building the store above a parking garage. In central urban areas, it's not, so they build up.