iOS apps have always been behind an Apple interface. I fail to see how registering a voice command is different from registering, say, a mailto: handler. There'll be guidelines (hopefully) regarding preferred sentence structure, because it's a basic need of such an interface.

Users may often not see the app – that's kinda the purpose of voice commands. But the interface isn't replaced by an Apple interface, its surface is simply reduced.

You'll say 'Facebook message mom' or something like it, and it's going to message mom. You won't see the FB logo, because you won't see any logo. You may see more your mom, though.

In fact, third-party apps will profit, because they are no longer second-class citizen compared to Apple-provided apps.

There are certain tasks that are predestined for Siri – such as starting A Nike+/Runkeeper/etc. run: easy one-shot commands that replace unlocking, navigating, opening, menus etc. I'd suspect if this were a major conspiracy, Apple would have opened the API earlier.