There must be some incredible data being mined by Amazon via Whole Foods. At the Whole Foods in Palo Alto, there seems to be an elaborate pricing experiment in the ice cream department. Entire brands (Talenti) are dropped in price 70%. Other times, particular flavors are reduced that much, sometimes less so. For Talenti, the entire brand is sold out. Some of the on-sale flavors go quickly or are also sold out while others are completely ignored, despite the discount (namely anything from Three Twins, who's blurb on their ice cream and their shop at SFO make them sound like assholes). Maybe 25% of the options in that section are discounted, and the amount of discounts varies as well, with a number of different steps like (80%, 50%, 35%, 20%, 10% or similar). Nothing else in the shop is stratified like that. Beer and wine might have 2% of the options on sale. Ditto produce and meat. Most departments offer no discounts.
Alternatively: Amazon has decided certain brands won't be carried anymore. Therefore those brands are getting steep discounts to clear the stock and Wholefoods' legacy contracts quickly.
To your point on beer and wine: state liquor licensing boards control retail pricing structures pretty heavily. In Tennessee for example (the state I’m most familiar with), the price of beer can be set at whatever, but liquor can’t be sold below cost and wine can’t be sold below a 20% markup over cost. It makes discounting a bit tricky, to ensure you stay compliant. Especially if you already have competitive pricing.
