I swear I must be the first (only) person to catch this, but I have a sneaky feeling there's a closet Star Control II lover on the Civilization: Beyond Earth Dev Team.
Check it out, they just released the pre-order bonus planets you'll get if you pre-order the game, and one of them is this:
Eta Vulpeculae b: A mysterious new discovery with unknown terrain.
Hmmmmm.... and Star Control players recognize this? And out of a million-billion star systems and planets available to use in their game, they choose Eta Vulpeculae b???? The site of the Androsynth disappearance and the appearance of everyone's favorite *Happy Campers*, the Orz ("Them")? Could this be a coincidence? Why pick, LITERALLY, that EXACT planet?
I know I'm onto something... if there's a robot or aquatic menace on that planet, it'll be confirmed!
Source: http://wiki.uqm.stack.nl/Bukowski