I suspect that saving the cost of managing AmazonSmile is the primary motivator. That's a lot of overhead! Two thousand pages of charities, most of which are collecting less than $30. I'd bet there are hundreds, if not thousands, of charities that Amazon was paying more to manage collection/disbursement than the actual charity received. (Or maybe not--there seems to be a minimum payout of $5.00, starting on page 1881.)
My point is they are trying to sugarcoat this as focusing on specific charities, whereas I believe total donation dollars is going to drop. In addition, I think Amazon is hoping to save on costs having to manage AmazonSmile itself.