I think you mean app store subscriptions. Apple Pay and app store subscriptions are two different things.
But I do agree with you; I see three likely scenarios:
1. An application offers two payment options: app store and standalone, with a "discount" given to standalone.
2. They change nothing
3. They remove app store subscriptions and force you to their website/app for managing payment/subscription.
If an app chooses option 3, this is where the user is "hurt". I don't see this happening often because I would wager that a service's subscription numbers would take a massive hit. Too many users are accustom to the simplicity that has been offered by in-app purchases/subscriptions.
But I do agree with you; I see three likely scenarios:
1. An application offers two payment options: app store and standalone, with a "discount" given to standalone.
2. They change nothing
3. They remove app store subscriptions and force you to their website/app for managing payment/subscription.
If an app chooses option 3, this is where the user is "hurt". I don't see this happening often because I would wager that a service's subscription numbers would take a massive hit. Too many users are accustom to the simplicity that has been offered by in-app purchases/subscriptions.