The apps talk to the world in a different way that normal native apps would. All communication goes through a Cap'n Proto RPC connection that is handed off to the app at startup. An executable is provided that knows how to bridge this to HTTP, making it relatively easy to port in existing apps, but the real power of the platform will eventually be exposed through that RPC connection. Inter-app communication will be through Cap'n Proto RPC, which is capability-based, allowing apps to expose APIs to each other and letting the user easily and security control which apps can talk to which other apps. Compare to Docker, where you can open ports, but don't have fine-grained control over capabilities. (Sorry, this really deserves a lot more explanation...)
Also, the idea is that you don't isolate apps, you isolate individual objects. So for Etherpad, each document is in a separate sandbox. This means that the platform can implement sharing for you, by doing it at the instance level. It also means that if I share a document with you, I don't have to worry that a security bug in the app will allow you to get access to all my other documents. Only a platform bug could allow that.
Finally, there's a nice web-based UI for installing and managing apps, so even non-sysadmins can actually run their own server.