The NYT lists represent the most influential bestseller lists in the country - even if their numbers have been proven to be somewhat inaccurate at times. (It doesn't actually use the sale numbers from every bookstores in the country - just about 3,000. And the actual methodology used to create the list is a secret.)
Still, being on the NYT Best Seller list creates massive publicity, and raises the stature and sales of any smaller books out there that land on the list. Like Oscar winners with the Academy Award Winner in front of their name, you very rarely see promotion for a NYT Best Seller book or author without that title out in front and in big, bold letters.
I'm glad that the list is trying to stay recent (although I've never really agreed with the staple of how NYT best sellers are judged - I'll stick with Amazon's lists for a more accurate take on what people are actually buying), and this will only push e-books further into the mainstream market. I think the publishing industry has learned from the music industry's mistakes - instead of trying to dismantle the new technology that comes, you must not only accept it but embrace it.