Emissary says: "+3 Cards / If this made you shuffle (at least one card), +1 Action and +2 Favors."
Its FAQ says: "First draw 3 cards; then see if drawing those cards caused you to shuffle. If it did, you get +1 Action and +2 Favors. It only counts as shuffling if at least one card was in your discard pile."
It is seeming way simpler, and true to those texts, if all that Emissary cares about is that you had that one card in your discard pile. Emissary cares if you shuffled; it says "at least one card" to try to be clear. Star Chart says "When shuffling..." I sure think players will expect that you shuffled; there Star Chart is doing its thing, which only happens when you shuffle.
So then: If you play Emissary with e.g. 2 cards in your discard pile, but then due to Order of Masons you have no cards to physically shuffle, Emissary doesn't mind, you still get the bonus. I'm glad that was just tentative before.