Here's my hypothesis of the Organoid system (Ultimate X) on how it came to be and such. This is essentially connecting Chaotic Century and New Century Zero (I really like to link series together, makes a much deeper back-story when the two stories are combined). Anyways let’s get to it:

Hypothesis

My main hypothesis on the Organoid System is that a while before the events of Chaotic Century, or even before the time when humans first landed on Planet Zi, the Zoidians were refining AIs as they had already mastered and befriended Organoids. During some testing, of the merging of Organoids into Zoids, they found some problems as well as possible benefits if they knew how to overcome these problems. The problems would possibly entail interface structure between the Zoid and the Organoid(Zoid Core interconnections), as well as power source conflicts. Once the Zoidian Engineers overcame these problems the benifits opened up to them, a fully sentient Zoid from the Organoid merge. But there was a problem, the power source conflicts and hidden interface problems. So essentially the organoid was permanently sealed and merged to the actual Zoid. Zoidian law probably found out about this and cut funding to continue research and testing on the Organoid merge. Which leads to about a few handful of Zoids which had the permanently merged organoids. Bit's Liger Zero would be one of them. After that Zoidian law made it a crime to attempt such merging procedures(As they considered it an offense to Organoid Civil Rights as Organoids were right up on par with the Zoidians) and the designs and research data was destroyed, not as a cover up but just as insurance for someone to attempt this. Year past and past and now we come to the first contact of humans landing upon Zi, long after the Organoid System Testing and the fall of the Zoidian civilization to the Deathsaurer.

Evidence

One large part of evidence is shown in Episode 23 of New Century Zero were Dr. Toros is talking with one of the mechanics after the Blitz Team's Zoids get a full inspection. The mechanic notes that his team found a black box within the Liger Zero and is shown to Dr. Toros on screen. Ultimate X

The black box looks mysteriously like the Skull of an organoid, as depicted with its protruding nose and pulled back eye sockets, roughly having the same structure as Van's/Fiona's Zeke, although you could also argue it has the same bone structure as Raven's Shadow or Hiltz's Ambient. I'm not sure about Reese's Specula as Specula's skull is more elongated than the other three organoids. I also must note that this particular organoid skull is not any of the four organoids from Chaotic Century, as the data and procedure of permanetly fusing organoids to zoids was lost for a years already.

Summary

Well thats my theory on the relation between the Organoid System(Ultimate X) and the Organoids themselves. I may come back to this to revise it if I find more evidence. Please give me your thoughts on it.