Oh... this makes things much clearer to me actually. The issue is that you don't want apps that impersonate other apps showing up. For example, if someone put an app in another market that could sideload to impersonate Facebook's intents and do evil-maid type things. In the new system it would become very difficult to install a fake Facebook that is able to convince other apps that it is in fact Facebook's own app. Google's announcement can be seen as them operating essentially like DNS for app ids and intents and making things safer for a multi-app-store universe.

For example, there is an annoyance that happens sometimes with apps that are distributed in both F-Droid and Play Store related to updates. F-Droid and Play Store will think they both can update the app (they have the same tld.what.ever identifier) but the signing keys only match the store they were installed from. I think F-Droid is now a bit more careful about this and only tries ones it has specifically installed. This is different... but somewhat related.

F-Droid in general is a model good actor as far third-party app stores go, but from the perspective that malicious app stores might exist you would want to try and isolate apps from each other (and prevent unauthorized re-distribution of tampered versions etc). I think what Google is doing forces apps in each store to be cleanly namespaced from each other and prevent collisions (accidental or otherwise). This lets each app store tend and be responsible for its own walled garden.