No, those apples are fresh. They're cheap because it's apple season. The gala apples on sale are probably too small to do well in long-term storage. Whole Foods isn't the only grocer selling those, either. I bought a bag and just noticed today that my office (a big Silicon Valley company who sources commercially) put out bowls of the same apples (they're conspicuously small and yellow for gala apples).
I don't get all this business about Whole Foods being expensive. I went to Costco, Safeway, and Whole Foods this past Sunday. Per usual, the packaged, vacuumed-sealed ground beef was Generally, for staples (meat, vegetables, canned goods) I've found Whole Foods to be no more expensive, and often cheaper, than elsewhere, unless I'm buying in bulk at Costco (e.g. a case of canned beans). Whole Foods can do this precisely because people blindly buy their premium products, like prepared foods. Whole Foods sells a huge volume of high-margin items. By contrast, regular grocers make their profit from low-margin staples. Thus, for staples Whole Foods will always be competitive. Moreover, because Whole Foods is upmarket their staples (especially vegetables and meats) are often of better quality if only so they don't detract from the overall feel of the store, and in any event they move quicker off their shelves and are thus often more fresh. Compare the butcher counter at WF to your regular grocer, assuming the regular grocer even has one. I can often get freshly butchered, hormone-free chicken for $1.99/lb (never more than $2.99/lb) at WF; at Safeway the only way to get that price is pre-packaged Perdue chickens.
Don't get me wrong--I've walked out of Whole Foods having paid plenty. But it's knowingly and by choice. And there are plenty of times where I've walked out of Safeway thinking, "WTF!?".
I'm not looking forward to Amazon's cost-cutting measures. If Whole Foods moves down market it means the premium shoppers will go elsewhere and stop subsidizing my purchases. Amazon can subsidize the prices, but I suspect quality and selection of staples will go down.