You can use the CocoonJS to do stuff you would only do on platform that CocoonJS supports. E.g. if you also ship your game to platforms that CocoonJS does not support and you dont want specific stuff to happen on those platforms.
See it as a hieraki. If you choose CocoonJS both your actions will be called on both IOS and Andriod. If you choose one specific like IOS it will only happen on that platform.
So CocoonJS is just 1 step up the abstraction ladder.