This begs the question: why didn't GOG incorporate the expansion if it's seemingly so easy to apply??
Probably because SMAX wasn't very well-received. I personally like the features it add and simply ignore the alien factions it add (as well as some of the more "broken" non-alien factions (*cough*pirates*cough*)), but I know a lot of people don't like it.
I also know that some people have had issues running SMAX on modern machines, for some reason.
Either of them could be a motivation for not baking SMAX into the SMAC release. Hopefully we'll see a SMAX release in the future.