I am pretty sure the Alpha/Beta key you got from KS will be revoked when the game launches. You'll still end up with three copies of the game though(two Steam keys from the CE and one key of your choice).
But I'm not sure anymore....I was only supposed to get one key for Dragon Commander and I chose the Vault, but then they gave me a Steam key for the full game too(not the Beta) which I don't quite understand why, maybe a mistake or something.
Guess I will have to wait and see, unless someone from Larian has anything to say about this. Not sure how often they read/reply on this forum.
Actually same thing happened to me, I have the game on steam, and I also have a copy on the vault.
On Larian vault I have one that says:
"Divinity Dragon Commander Imperial Edition"
and one that says:
"Divinity Dragon Commander Imperial Edition Addon"
And on steam I have one that says: "Divinity Dragon Commande Beta"
and one that says "Divinity Dragon Commander" (Which also has the Imperial edition as "DLC".
Edit: Interestingly enough that seems to indicate I can still install the beta version of Dragon commander on steam. Don`t see the point in doing so, but It seems it`s possible.