As far as I am aware, the Evolving buildings available in the Magic Academy will not change until the next recipe refresh, which does not happen often. The Phoenix bases are there right now because of the new Spire prize set, so if this feature change is popular and they decide to do a different Spire prize set including Artifacts in the future, it is probably safe to assume that the bases for that particular Artifact type will become available again.
The Spire changes were popular on Beta, but what Prize sets the future brings will depend in part on how it is received in the live worlds.