SMAC and the Call to Power series were made by different companies than the main Civ series, even though, through the process of the various sales and mergers since, all the rights related to them are, I think, in the same place now.
SMAC was made by the same people (at least, some of the key people) that made Civ I-II, at a different company (Firaxis) from the one then producing and controlling the IP for the main Civ series (MicroProse) who had, IIRC, laid them off.
Several acquisitions and spinoffs of everyone involved, and all the rights are now with Take-Two, of which Firaxis is now a studio under the 2K games umbrella.