Alternative in-app payments is about third-party developers receiving money in apps without the manufacturer getting a cut; alternative app stores is about third-party developers receiving money for apps without the manufacturer getting a cut.
While they aren't _necessarily_ coupled, the bundling of an app-store and cloud services such as payments, notifications, and more, along with vetting (for security issues) does seem of value. One can certainly imagine third-party app stores including similar requires to apple. I can imagine a Yandex store, Tencent store, that both require you to use their payment platform if you want to host an app in their store. In fact, being integrated into a cloud-service-vendor's ecosystem might a reason to chose a particular store in the same way the Play and Apple are part of the decision today.
Not necessarily alternative app stores / install mechanisms, which is a separate issue.