I don't think it'll shift as quickly or as hard as you expect. I imagine this will just be where some companies strongly urge users to use their native payments, but there will be some small "use apple pay" button (possibly mandated by Apple, possibly not).

On top of that, many may not bother at all. setting up a payment vendor isn't trivial. Some may be happy to let apple keep 30% of the gravy for that convienence.