Where do you live? My experience comes from wealthy suburbs in Los Angeles and Miami as well as the Bay Area in general but different markets are different.
There can be many effects in play like marketing, staffing, and real estate prices. The Vons I mentioned is actually getting more expensive while the Pavilions is getting cheaper because the Vons cut back on cashiers. The longer lines have caused many of my friends and I to start shopping at Pavilions, which is causing a death spiral as Vons tries to charge more for produce just so they can pay the overhead on the building (the Vons location costs twice as much in rent as the Pavilions because of lease terms and the outdoor mall it's in, despite being across the street).
I would imagine that different markets make a huge difference.
My only two points of reference are Denver, CO and Kansas City, MO.
In Kansas City, Whole Foods produce and dairy prices were anywhere from 100-200% more than their Price Chopper / Hen House / Hy-Vee equivalents. Meat was marked up around 150% from their commodity supermarket price with a marked increase in quality and variety.
Denver has a roughly 30% higher cost of living than KC, and here the Whole Foods / Sprouts produce and dairy goods prices are competitive to slightly-higher than the King Soopers (local Kroger subsidiary) / Safeway prices. Meat is marked up around 100% from the commodity supermarket price, but with the same distinction in quality and variety.
This is all anecdotal and subject to my terrible aggregated memories of shopping trips, but this subject is fascinating to ponder.
There can be many effects in play like marketing, staffing, and real estate prices. The Vons I mentioned is actually getting more expensive while the Pavilions is getting cheaper because the Vons cut back on cashiers. The longer lines have caused many of my friends and I to start shopping at Pavilions, which is causing a death spiral as Vons tries to charge more for produce just so they can pay the overhead on the building (the Vons location costs twice as much in rent as the Pavilions because of lease terms and the outdoor mall it's in, despite being across the street).