Is there a way to have an article that lives in multiple collections launch to a different object state within the article depending on which collection it's launched from?
No. You cannot target a specific state of an MSO in a link.
Well, that's kind of a bummer.
The new Context API would make this possible with an HTML5 article. If you can replicate your MSO behavior with HTML, you can totally do what you want.
Problem is it's an InDesign to AEM mobile article. No dice, I guess.