Yea, the base game already has so many options, that adding the expansions would probably just make things more confusing to someone learning the game.
However, it should be safe to turn on the Zenith Reminant stuff. It is much more polished and balanced than the others (understandably so, it is the oldest expansion after all), and adds a bunch of stuff that is very, very useful that has sort of settled into the "metagame" almost for granted.
And possibly most importantly for a new player, the things it adds aren't really all that "different" compared to the base game, it doesn't really add a huge new aspect (other than the optional Golems) to learn. The other expansions add new, somewhat tricky mechanics to learn. Plus, the ZR expansion gives more "boons" for the humans than it does the AI on average. (Golems, Z ship caches, distribution nodes too I think).