Heh. Well, as I said before, we are looking at a recount of historical events as interpreted by Blackarachnia - most of which is historically accurate, but some things aren't.

The Autobot-Decepticon conflict had been waging on Cybertron millions of years before arriving on Cybertron - and continued to be waged for an additional four million years while the occupants of the Ark remained in stasis. In the G1 comics, Lord Straxus rose to power and the Autobots were driven underground (re: Autobase) under the leadership of Emirate Xaaron. In the G1 cartoon, Shockwave ruled over Cybertron in Megatron's absence and there was again underground resistance formed by Alpha Trion.

Even Blackarachnia's recount of how the Ark crashed on Earth wasn't entirely accurate. In Blackarachnia's recount we see the Nemesis engaging in ship-to-ship battle with the Ark above Earth, shooting down the Ark. In both the G1 comics and cartoon this didn't happen - the Decepticons boarded the Ark and fought the Autobots inside, and then the Ark crashed on Earth. Later when Megatron and Blackarachnia entered the Ark we see that there are both Autobots and Decepticons lying in stasis; awaiting reactivation in 1984C.E., which is historically accurate - but contradicts the part of Blackarachnia's recount where the Ark was shot down by the Nemesis.

But Blackarachnia's not exactly a historian - and while she does possess impressive knowledge of historical events, it would have been knowledge that she acquired on prehistoric Earth since that was where she was "born" -- she'd never been on Cybertron (at the time) to access more extensive historical archives.