It depends. There might be a certain point in the game that we have to pass before we can use the Pokemon bank. If that's the case, it won't be possible but if you can use the bank as soon as you start the game then yeah.
But my guess is we'll have to wait to use the Pokemon bank.
I see where you're coming from, but seeing as it's an external app...maybe it can store the pokemon in your box in-game so all you need access to is a Pokemon center' PC