Yeah, but when you bring switch a Pokémon in (in a single battle), it moves to position 1 and whatever was in position 1 moves to its former position. This will affect what Zoroark chooses to become.
So then at the end of battle, the order is "restored" to whatever it was? That would only work if the game remembered the original slots pokemon were in before the battle, which is the list Zoroark's Illusion should use.
I sincerely hope Nintendo isn't dumb enough to make it work based on current battle positions, as that would be confusing to the point of being ridiculous.