Sometimes.
For instance, on The Way of Kings, we asked for colored endpages. At first Tor was hesitant; they’re very expensive. We kind of begged a bit, then showed them these cool pages and talked about how great the book would be with them, and eventually Tor decided that they would go with it. One of the aspects of doing colored endpages like that is that generally you have to use the same endpages for the entire series to offset the printing cost. So those same endpages will likely show up in some future hardcovers. We did get new colored endpapers for Words of Radiance because Michael Whelan felt that Shallan needed to be featured as prominently as Kaladin, so he painted another beautiful picture, and TOR just couldn’t refuse something like that.
As I sell more books, I get more clout as an author. I can do things now that I never could have demanded or even asked for as a new author. That’s one reason we’re doing tenth anniversary editions of each of my books. I’ve proven that we have an audience that will value beautiful new art. The marketing departments are also collaborating with us on the cover art for my books. Earlier in my career, I had no say at all, even on terrible covers.