But wasn't that conflict manufactured by the Reapers? The Geth fought the Quarians in the Morning War out of self preservation. Then they were said to retreat into the Veil for 300 years. They were not heard of again until Eden Prime, where they were being indoctrinated and used by the Reapers. It was not a fight that they chose.

Legion's loyalty mission in ME2 demonstrates that autonomous Geth want to avoid war. The Geth influenced by the Reapers want to exterminate organics because they were convinced it's the only way they could survive. And in ME3 they ally with the Reapers because the Quarians attacked them first.

I'm not trying to say the Geth aren't responsible for what they did. But synthetics surpassing and then destroying organics as the Catalyst insists was never the driving force of the Geth conflict. They acted out of survival as any organic species would. As every species does in ME3. It's a side theme for sure, but different species coexisting in general is the much larger common theme across the trilogy.