Not sure I agree with the conclusions of that article. Konrath is not a typical self published/independent author. Konrath is a commercially published author with name recognition and a commercially published back list. Yes the publisher is taking a big chunk of the money but I doubt that an author who was not in Konrath's position would be doing so well from sales. I think that in the future unless publishers start being more generous with ebook royalty rates we will see more authors in Konrath's position self publishing their backlists, new fiction they don't think can be commercially published, writing guides etc.
On the NYT article colour me surprised that publishing houses are trying to assert they own the rights to something that didn't even exist when they bought the rights. Authors & their agents are going to have to pay close attention to contracts to make sure publishers aren't buying rights for things that don't exist now but may in the future.