That's what I have been thinking.
Say I shopped at Boots, would it automatically add Boots points to my Boots card when I payed with one of my debit/credit cards on Apple pay. I'm guessing that's something that we will have to wait and see.
Also if Apple are offering store cards then these store cards are going to collect your spending habits data, it's what they are there for.
Boots have said they won't be adding the Advantage card to the iOS app anytime soon so I can't see them being on board at first - I know you just used it as an example. This would be good functionality though. Loyalty cards is the reason my wallet is so fat.
On the topic of Boots - I see that they have said on Twitter that they will have the £20 limit. Disappointing when they are a launch partner.