It wouldn't surprise me if the planet turns out to be some lifeform. Not a sentient planet but an organism on it's own.
It makes totally sense, I mean, look at the zenith. They are huge! Okay, they are cyborgs but they still are very big and maybe their base was big to begin with (since we never saw the original form of a Zenith we don't know).
Spire are also big (Dreadnought anyone?) but they are mineralbased (crystals do also "grow" but I forgot how exactly).
So, what is the pkanet actualyl? A planet with a soul or it is a big alien lifeform where other races thought "Oh, look, a planet, let's live on it!". That would explain some stuff.
Planet Rage: Well, the "planet" is angry about the parasites on its body and want to get rid of them. If you see a tick biting you, you remove it. Thoraxians are in that way more of a symbiont. They take care of the "parasites" and in return the planet let them live on it, feed from them etc. other life forms on the planet may also be symbionts or act similiar in a way to our bacteries.
The "Transendence" ending would lead to replace the fucntion of the Thoraxians with your race. the planet ackknowledges that your race is more fit for the role of removing the parasites, including now the Thoraxians that go on a rampage just to stop you.
Other victory conditions may lead to a "peaceful together" where you don't try to compete against each other and the planet don't care enough anymore because they don't hurt him anymore.
That's of course my own little theory/fantasy but comparing it to AI War I think it would be possible. Also, I read a short story with a similiar setting.
I don't know the exact plot anymore but overall it was about two astronauts that discover a new planet, decide to land on it, making some research, taking off and then they got caught by another alien race that shows them that the "planet" is acutally a giant alien that they worshipped and the two astronauts killed it with the fire of their rocket and their resaerch on it.