It's definitely an interesting one, and a bit minboggling without them actually meeting each other. That said, I'd favor Afterthought here. I keep running the scenario in my head, and his precognition keeps winning.
In short, Fantomex will have to act eventually, at which point the jig is up. Afterthought will know in advance, effectively nullifying the advantage. Even if Afterthought falls for an illusion, he'd know it was fake before Fantomex could actually act on it.