Karza was in fact an Atlantian. He rose to power and Godhood during the Atlantian Great War, which lasted over a Thousand years. Karza defeated in battle with help one of the Cybertronian Gods. Losing an Arm and Leg in the battle which would not heal. Replaced those with artifical ones. During the war, he discovered many things. Primius himself asked him to join them. He did so without thought. Primius then transformed him into a being like themselves.
Many Atlantians turned to Karza for worship then, and the cybertronians enjoyed a brief time as one of the Atlantian pantheons. It did not last long. 300 years later, Something happened to Atlantis itself. Cybertronians lost their connection to Earth. At the Start of the Age of Industry is when the Cybertronian returned to earth for the first time. Their arrivial triggered something in mortals. Machines once again started to become known again. If this is true or not, who knows.

"i'm a Big Fluffy Puppydog, with bad teeth" - spike