They allow linking to external apps using external payment systems and external installation processes. That's not a great solution for small teams that just want to build apps.
Making a website, creating a setup file, and setting up payment processing and license delivery really isn't much effort - especially when you don't have to pay a 30% commission to the app store.
The benefit of developing for app stores is the extremely smooth process for users to purchase, install, and update apps. Imagine how popular Steam would be if all they had were a bunch of simple games available to purchase, along with links to AAA titles on publisher websites to go buy and download separately.
