Stores should be included for both clearly. It's all part of the overall density.

Parking garages are expensive and still take space. More people driving also inflates roads, around stores just as much as elsewhere.
And the fact that suburban sprawl stores simply don't build garages and instead have massive lots should definitely be counted into density.

If you call it housing density or suburban density or any other density I don't really mind, but this is the metric to cut down to make places nicer. And cheaper. Since ultimately all of this is also paid for with the economy, i.e. the peoples money.
If your road bill is small but your store's bills huge, you'll still pay more.