There are some pretty sophisticated ventilation systems out there. Take Norstrom for example. Their stores have a special fragrance that is used throughout the store in order to keep the shopping experience pleasant.
Apple stores I believe, do not have such a system. Supermarkets keep their temperature low to keep the packaging odors from being noticed. Its not the food but the various types of plastics that have an unctuous odor. People too have various odors, clean or not. Cool temps help with that.
Every Apple Store I've ever visited had or has a disagreeable fragrance. Regardless of the location or the people inside the stores. All just didn't have a nice smell to them.
I think the overall chore, besides architecture and layout, is for Apple to be aware of what needs their stores have in fragrance management. Its pretty clear this is something quite well overlooked either by their present equipment or their management. It certainly would enhance the Apple Store experience and make remaining in one for some time a pleasure.