Wait...do we have three keys in total? I'm confused...
If you have the CE, then yes. The CE has 2 Steam keys, and you still have the digital version that you can (will be able to) choose between GOG or Steam.
I remember reading that the kickstarter keys for early-access (the alpha and beta-keys) will be deactivated on release. mine still works, but says it's beta.
They changed how that will work. Now by default the alpha/beta keys will just upgrade to the Steam version, but you can revoke the key to get either a GOG key or a new Steam key (if you gave away your alpha code).