The IDW timeline is very weird. If you read More Than Meets the Eyes, you see his origin and what he is like in the present and it makes no sense how or why he was a bloodthirsty genocider in between those periods.

The writers had the baggage of the countless past iterations of the franchise where the war is defined in very simplistic good vs. bad terms. I think they just chose to ignore its deeper implications. I don’t mind it though because it makes More Than Meets the Eyes a great read if you are not irked by the inconsistency in the continuity