I don't work for Apple, but I think they would point a developer to in-app purchases (IAP) as 'the way' to do paid upgrades.

Still, auto-renewing IAP subscriptions are limited to a narrow class of applications (see AppStore review guidelines #11.15), forcing most to use churn-prone manually-renewing subscriptions. Outside payment systems are largely prohibited for digital goods under #11.13. The combination of these rules forces multi-platform subscription based apps (i.e. Autodesk's 123d-line of apps) to juggle multiple payment systems. Integration between those payment systems is often weak due to lack of a published web service or hook-system for IAP.

AppStore review guidelines can be found here: https://developer.apple.com/app-store/review/guidelines/#pur...

The state of in-app purchases leaves much to be desired.