Well, for what it's worth, I looked at it as well and can confirm that it appears the Alien Crossfire 2.0 patch is indeed missing. From the file dates and the files present, it appears that GOG took the Planetary Pack ( Looks like it is at version 1.0 of SMAX ), and applied the SMACXP patch ( which just updates the SMAC files ), and then did their magic to the executables to make them run in more modern operating systems.
Personally, I just took the Alien Crossfire 2.0 patch, unzipped it, and copied ( and overwrote ) all the files into the game directory except to the two executables ( terran.exe and terranx.exe ) and the .icd file ( although I don't believe the GoG version uses this file ). This appears to update the game to 2.0.
I did notice the the SMACXP patch doesn't appear to affect any SMAX files, so the only real reason to install it after the Alien Crossfire 2.0 patch is to update the original SMAC executable, which isn't necessary if one retains the GoG updated .exe.
The only real concern I would have to updating the game in this fashion is if the Alien Crossfire 2.0 patch made some important update to the terranx.exe file, which wouldn't be fixed in the current game download, as the .exe appears to be based on the version 1.0 .exe. I use Scient's unofficial SMAX patch executable, however, and I haven't had any problems yet.
I apologize for the wall of text, if anyone is still reading at this point :-).
Post edited January 03, 2013 by davejones3364