Changing things on the back end so that Amazon isn't undercutting the game stores was one step. The early release window and exclusive covers are another. And not massively undercutting the game stores with digital releases is a third. Could WotC make a lot of players happy and some good short term profits if they marked down digital releases to an equal profit margin? Sure, but in the long term it'd kill the game stores, and that's eating the seed corn. They need the game stores to keep D&D healthy, so the game stores are protected.
I'm curious. I agree that WotC wants a healthy game store ecosystem, though I am skeptical that D&D sales in themselves, while significant, are a cornerstone of many, if any, stories. We are blessed to have quite a few in the Greater Victoria area, and from what I can see, in this region they seem to be mainly supported by collectible card games, board games, and Warhammer, with RPG-related stuff maybe a distant fourth. I'm curious as to what actual game store owners who post on this site see.
More to the point, I don't see much evidence that they are artificially keeping digital sales high to help out FLGS. Their price on digital sales seems to be around 40-50% of the price of physical sales. That's around the same as what Amazon charges for a Kindle title on new release (I recognize that there are all kinds of sales that happen, both on Amazon and DDB, especially of older titles, so these are very rough figures). But the given that WotC is not the middleman on sales, like Amazon is for Kindle, it strikes me that WotC is probably keeping digital prices relatively high
because they can. Why charge less when the market will pay you more? Especially given that they have near control of the market, in this case.
TLDR I don't think WotC is keeping digital prices somewhat high out of altruism.