The Pretender Autobots were robots in control of their bodys, they just gave the few humans control of the "Transectors". Chromedome made an apperance in the beginning of the series contacting Metal Hawk and the others, indicating this group(Pretenders and the Human Headmasters)was just another branch of Autobots on Earth. There were still Transformers on Cybertron, and later on(well i don't want to spoil anything for you),well let's just say, some other sentient robots show up. I hope this clears it up your question a little.
Man, I really love Masterforce!!! I hope you are enjoying it as much as i do!!!!!
