Great question.
Ordinarily, WordPress tries to add a canonical link during the wp_head action. What Events Calendar PRO does – if a single, recurring event is being viewed – is remove WordPress’s callback and substitute its own callback (you can see the relevant code here and here).
So there’s no reason you couldn’t add your own code along similar lines – knocking out our callback that generates the canonical link in those conditions and replacing it with your own – of course if AIOSEO also has logic that impacts here you would need to carefully workaround both systems.
I hope that helps 🙂