My local stores do, it's not displayed so call them or ask in person. Make sure you want the ultimate version and tell them the specs. Some employees have no clue what you are talking about.
Another hint to tell whether a particular Apple store carries a particular configuration, is to look at the plastic display on the benches.
To share my experience, it was until I glanced through those display that I realized they do carry the ultimate 11" MBA. I cancelled the online BTO order in the Apple store and bought from the store directly.
Apple Store in Pacific Centre (Vancouver, Canada) has them.
They, after getting approval from AppleCare and the manager, replaced my first MBA (ordered online) with an in-store model (same specs... 13" / 2.13 / 4GB / 256GB).
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I was surprised to see that Fairview mall in Toronto has every configuration advertised in-store on the little price cards beside the demo models. From Base on up to the so-called "Ultimate" version.