Like others have said I'm sure it will be like Pacific Fighters. You can play it standalone or merge it with your CloD install.
I'm sure they will also release a "gold pack" as well containing both so people late to the party can get everything they need all at once. That's how I originally bought IL2
I think I bought a gold pack of Forgotten Battles combined with the ACES expansion pack.
You have to assume the new game will be more polished, hopefully they have learned their lesson.