If nothing else, uniformity doesn't add as much value to a brand that isn't selling its own product. Nobody really worries that the copy of a book they buy in one shop will be different to a copy bought in another. There are likely some benefits to consistency, like a familiar store layout or knowing that a shop will stock a good range of books, but these are kind of ancillary to the product (and my experience is that these things aren't that consistent across big chains anyway).

There is a great book shop in Dublin, Ireland called Hodges Figgis. It was bought by the UK chain Waterstones in 2011, but you wouldn't know it - they wisely decided not to interfere at all with such a locally beloved brand.