They both eventually got their asses kicked by a dude with a Latin name...

 

This has been hinted at with Exodus and Exiles. The name Autobot didn't arise until Prime used it, IIRC. This is more in line with G1, how Autobot and Decepticon emerged simultaneously based on their functions in Quintesson society.

In IDW, it's not clear when Autobots became a separate faction from Cybertronian. When government and the command structure were established, is that when they called themselves Autobots? Were only the officials called Autobots? As we saw in Drift, some Cybertronians left during the war and became a neutral faction.

Speaking of the Drift comic, where is Lockdown?

 

In Ongoing issue # 23 (I think it was) Optimus takes the term Autobot - it was previously used by other species as an insult to Cybertronians