- It would explain why they run into so many eccentric or outright insane Abh.
- The genetic engineering wasn't self-imposed. They were created, in their own words, as living machines, for deep space exploration by an ultra-nationalistic Japanese splinter faction. They just deliberately keep their genes within the original parameters set by their creators. Doesn't negate the idea, but it does shift responsibility.
Why has the God-Emperor of Mankind not stopped the Abh, or sided with United Humanity? Because He knew that Mankind would have to be united before the first alien contact and he decided that the Abh were the best choice for achieving this end. And he knew that Mankind would need the innate advantages that Abh-commanded spacecraft would lend Humanity in those inevitable wars. And their style of government suited his philosophies better. Thus, he sided with them.
Contrary to what one would expect, the Abh, or rather their distant decendants, still survive to the present era. Specifically, as the Guild of Navigators. The Abh ended up adapting themselves to being able to navigate the warp after it's discovery. They needed this ablity to keep up with such foes as the Orks and Eldar, as well as the many unnamed races that mankind faced in the Dark Age of Technology.
The opposite is also possible; the Abh are not the precursors to the Empire of Man. They are the Iron Men, defeated by the Emperor and uniting mankind. The war with the Abh is the force that is uniting the other disparate elements of humanity together, by providing a serious "external enemy" that forces them to push their various cultures under one ruler. The Abh, while technically human, are considered machines by this pre-Imperium, and will be recorded as such when this conflict is placed into history. While history will remember them as the "iron men", another term will arise during the conflict to describe things that are "human" without being entirely human. It's origin will be entirely forgotten by the time the Empire of Man has reached it's apex, but anyone that knows the actual truth will recognize the significance immediately of the term: "abhuman".
During this war, some of the philosophies exposed by the Abh will be absorbed by integrating captured "national" Abh, replacing their equivalents in the United Mankind under the careful guide of the Emperor. By managing to get both the obvious core "pure humanity" of the United Mankind together and adopting useful ideas from the Abh, the Emperor can both have an empire that is firmly established as "Humans first and foremost" while also managing to keep whatever necessary cultural ideas are present in either side. The Abh would be poorly suited for this, as they do not culturally integrate or force new planets to do so; such a non-interventionist attitude to culture would make it harder for the Emperor to spread His message. And the United Mankind's character assassination of the Abh by accusing them of being machines, coupled with the Abh saying it is essentially true, would make it harder to push the idea of an Abh-based "Human Empire" on those of the United Mankind that had accepted this. Almost impossible when coupled with the Abh's lack of concern over planetary culture. The Abh may have ideas closer to His own, but their policies would not be able to force together the Imperium.
There are a few "survivors" of the Abh race in the later era, but the people in charge of their design don't know anything about the history of the process that creates them. These "Afriel Strain" warriors, genetically based on the DNA of Imperium heroes in a proccess that manages to render them pale skinned, nearly-white hair, and eyes that have no natural color; someone apparently managed to save some of the information used to create "genetic" Abhs, but no record exists in the future to link the process that creates the Afriel Strain to the original process that creates the Abh. Only one person would be old enough to know, and He is indesposed.