Stone-ground flour retains more of the wheat germ and bran than the roller-milled white flour most bakeries use, which changes both the flavour and the way the dough handles. It absorbs water differently, ferments a little faster, and gives a loaf with more colour and a nuttier finish than a standard white sourdough.
It also costs more, and that cost sits in the price of every loaf on the shelf rather than being hidden somewhere else. We'd rather be straightforward about that than switch flour quietly and let the bread get quietly worse instead.