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SoMa Costco has the parking under the store. It’s just economics.

On the other end of the spectrum, the notorious (in the Bay Area) Sunnyvale Costco actually demolished a nearby restaurant just to expand the parking lot.

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The restaurant was one of those “all you can eat” salad bars. It closed during the early part of the pandemic and had been vacant for several months with no buyers, if I recall correctly.
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Put solar panels over ‘em
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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?
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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.
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Only because stores that have large parking lots are in cheap land areas that are hard to reach by bus, bike, or anything except a car really. Where one can comfortably walk to a store, giant parking lots are awful.
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Indeed, and in defense of Costco, you don't go there by bus or bike anyway because you'll be coming home with 200 pounds of stuff. Target is different for me. I hop in there for one or two odd things that I need, likewise the nearby grocery store. A side effect is that I don't waste money or space on stuff that I don't need, because I can always hop over there in a jiffy if I do need it.

In lieu of Costco, my family buys all of the big and non-perishable stuff at a giant discount supermarket that's closer to the edge of town, or at least it was until other stuff got built up around it. But we try to minimize the number of trips.

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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.
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I have yet to see a Costco not filled to the brim.
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It's quite efficient use of land. Costco parking lots tend to be full, people tend to leave Costco with full carts and go once or twice a month. Direct to consumer warehouses should be encouraged not discouraged by the environmental social use advocate kinds of people.

It results in fewer miles driven and more being done per mile driven. Each parking space gets more done per parking space. There's less retail worker overhead and the people that do work are paid better and have a higher quality of life.

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The problem isn’t the efficiency of car use, it’s car dependency. If retail is only available in the huge units it’s impossible to access those without a car. And if people end up owning cars, even against their will, they will end up using those daily.

The goal is to avoid the car-centric lifestyle, not to optimise it. Maybe that is a totally utopian idea in the us, though.

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This is in comparison to the delivery center methodology by e commerce where the land use for delivery driver is somewhere further away from what is needed for community events, and every delivery truck is filled to the brim, way more full than what each consumer vehicle would be filled up with?
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Big trucks filled with stuff delivering a few things to each of many places is less efficient than personal cars delivering big loads with lots of things to one place.

Your SUV with a Costco haul is probably driving less distance per person and carrying MORE per person while being a smaller more efficient vehicle.

Amortizing fuel per item or distance per item I'm betting the personal vehicle wins while also being better able to deliver perishable/frozen items.

(also the likes of Amazon are terrible to employees in order to make margin while Costco is the opposite)

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