The ominous council of vague evilness.

Considering that assets for large and small tentacle meteor enemies are present in the game files, there's definitely more than one of those Earth-devouring beasts about. Again, my guess would be like Phaaze/Leviathans from Metroid Prime: tentacle planets produce tentacle meteors, which then crash into other planets and convert those into tentacle planets, too.

 

They are just trying to prep the universe for the inevitable tyranid invasion

 

I'll die laughing if the monster that destroyed earth was summoned/created by the penguins all along. It'd be like a twisted inversion of "So long, and thanks for all the fish."

 

xD
Also, Greenfinger and the other figure heads are actually Penguins too.
The Starbound universe is controlled by Penguins, and Penguins only.
The only reason why they come to you when you craft the distress beacon is because they want to 'test' your characters abilities. If you prove to be a potential threat, then the big shots will come in and 'experiment' on you. The 'heroic tale' you thought you was living was a lie.

 

Wild guess: they are all the same guy/entity.

Final Boss = Big Ape = Kluex = Greenfinger = ...