I think Petek got it right. I play SMAX with the original seven factions. The human side of the story is the same as the original but the expansion adds a few new technologies, a few new kinds of native life forms and some game balance tweaks among other things.
I think I prefered SMAC alone where the alien artifacts were just a mystery. SMAX exists pretty much solely to explain those mysteries and make the aliens playable (in addition to tweaking and adding more gameplay content). I'm sure many liked to discover more about the grand design purpose behind the 'Planet', but I thought the setting was good enough when it was just humans trying to assert themselves and their ideologies on a new frontier.
I think SMAX is a very impressive expansion. It is not a new campaign or a spin-off, it is additional story elements and game contents added on to the original. It is kind of like a director's cut that includes story arcs omitted in the theatrical release, though this is not a perfect analogy because there are some differences in key personel developing the original game and the expansion. Perhaps it is not exactly how the original designers had intended the SMAC universe to be. No matter, because SMAX is an official game and so it is also true canon.