I have noticed that B&N tends to stock Atlas along with a lot of other "required for school reading" before the start of the school semester, as with many other standards such as Catcher in the Rye. B&N certainly charges retail. I do not remember seeing this ten years ago, or when I was in HS in the 80's.
The size of ARI's free books program is presumably a matter of record, and you could ask them (don't tell them you heard the suggestion here). In the meantime, I'd guess that it's a few thousand books a year, not more than 2% of total sales.
