From what I could find, it does seem that major retailers back in the day (CompUSA, Circuit City, etc) were only making 15% margin on software sales. This is much lower than other product categories - but also software didn't take up much floor space.
It coupled the small floor space with high prices, and an extreme overall easiness of management (low weight, resistance to small impacts, possibility of stacking, etc).
So that margin not only had to pay for small management costs, and had small opportunity costs on the floor space, but it also was divided by a large unitary price.
its agency model vs retail model. Recall - Amazon hated the agency model, where the publisher sets the price (and 30% cut goes to app store - Jobs sold this as amazing deal). Retail model the retailer sets the price, and the publisher is guaranteed the wholesale price. Amazon preferred the latter because they competed on dynamic price setting. this was so long ago we forget.