Meerkat makes it fairly clear that "everything that happens on Meerkat also happens on Twitter" – and the comments on a stream only go to Twitter as replies to the original invite tweet.

That's not 'automatically… to many users" but specifically to those viewing a thread, and only when individual users compose individual replies. It's not a clear violation of the quoted policy… if at all. And as you note, that's not the behavior Twitter has started.