If one has multiple copies of a book, say 5 or more, they can take up less shelf space cover-out than side by side, depending on thickness... which allows you stock a larger, diverse inventory while still having copies in stock for the popular titles. Also, if a book is a very popular book, it's worthwhile to have it cover-out so that folks can quickly locate it. That doesn't mean the store focuses only on mass market, but instead focuses on customers: some want the popular item, so make it easy for them and not be out of stock on these, and some want more depth, so try to stock as deep as you can on the shelves.
For many stores across many industries, having enough stock of popular items subsidizes the ability of the store to stock rarer and less-often selling stock.