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).
That is correct.
Actually same thing happened to me, I have the game on steam, and I also have a copy on the vault.
At one point Larian said they would like to have Steam keys for all the games sold through the Vault (presumably people would be more likely to buy directly from Larian that way). I don't know if that is still the intent.
There was an issue with the GOG keys for some of the pre-order and retail copies of Dragon Commander, so the Imperial Edition Addon was added to the Vault as a temporary fix while that was sorted out.
Steam seems not to be set up to remove beta entries that are no longer useful.
