The article talks about Google working to make it easier for users to install 3rd-party app stores; I'd hope that allowing automatic updates would be a part of that.
Unclear if Google would be able to ninja that in to older phones as a Play Services update. My guess is that they probably couldn't since that's pretty fundamental to the OS's permissions system.
They could offer a Play Services API that allows app stores to update apps which the user previously installed through them.
As Play Services already has an API and the permissions to replace installed apps (although this API is currently only available to the Google Play Store), and as Android already tracks from where an app was installed, this would be easily possible.
Unclear if Google would be able to ninja that in to older phones as a Play Services update. My guess is that they probably couldn't since that's pretty fundamental to the OS's permissions system.