Here is an idea for a book.
Colonists are selected for intelligence and physical attributes--strength, agility, endurance. Not for any specialized skill set. They are injected with a retro-gene set that causes them to devolve while in cro-sleep. When they awake the ship AI releases them on to the colony world. Kinda/sorta like Planet of the Apes in reverse. They aren't devolved back more than a few tens of thousands, or hundred(s) thousands of years.
Also prior to release they are reinjected with a reversal gene set that will affect the next couple of generations.
The AI has projectors, etc., that sets itself up as "god".
A random thought.
I like your idea a lot. Author Gene Wolfe explored a similar theme in some regards in his book Nightside the Long Sun. His characters have gods to contend with and to help them in that story. Wolfe's stories are refreshing because he tends to write from the first person and your understanding of what is going in tends to clarify as the character's own awareness of reality increases. I like the "dawning realization" style of plot development because it feels more natural - like reading a detective novel, perceptive people can sometimes figure out what is going on before the narrative reveals it overtly.
Some of the details of your story-line might be tweaked to bring them into line with scientific fact. For instance, human genome has not altered appreciably since about 4 million years ago when sapiens sapiens split off genetically for good from the other proto-human sub-types.
Most of the evolution that human beings have gone through has been cultural and psychological in the last 20 thousand years. To find a significant genetic event which fundamentally altered human morphology one would likely have to go back about 200,000 years when the brain size seems to have greatly increased (probably due to turning the corner in the starvation problem). Human beings nearly died off several times in the span of time, mostly due to famine (as far as archeologists can tell). Once humans mastered social cooperation and tools, we could prey on other animals (herbivores) which were more efficient at foraging the abundant vegetation than we, and defeat any predators. Those capabilities filled in the last key pieces of the puzzle that would make Humanity able to avoid extinction handily for the rest of time and take our place at the top of the food chain permanently.
NOTE: The above event is represented in dramatic fashion in the film 2001: A Space Odyssey although it is placed much further back in time (millions of years instead of thousands). Likely something like what is portrayed in the movie could have happened in distant prehistory, but the anthropological record seems to indicate that the problem of starvation plagued proto-humans and nearly snuffed them chronically until humans achieved social cooperation skills and essentially started hunting in organized groups with fairly sophisticated weapons and building at least semi-permanent societies and primitive structures for shelter (circa 30,000-20,000 BC). Humans are like ants in the sense that we are social animals, we are not truly superior without social systems to support us.
The explosion of brain size (discussed in research into human brain evolution published in Ghost in the Machine, by Arthur Koestler) 2000 centuries ago was mostly in the cerebral cortex due to the ability of well-nourished humans to experience a quantum increase in neural density (because we finally had the calories available to develop it in infancy/early childhood and could defend our young from early death). Humans got a lot more intellectually capable in all probability at roughly the same time and never looked back (relative to the other mammals). This event is portrayed with dramatic effect in the fine film Clan of the Cave Bear (with the magnificent Darryl Hannah in the lead role, before she lost both her looks and her mind).
The other great fundamental change in consciousness likely occurred about 12,000 to 8,000 BC, when examinations of cave paintings and later hieroglyphics indicate that human beings started developing an operative understanding of being separate from our environment and the difference between the waking state and the dream state.
Even as late as the ancient Egyptian period, artwork indicated that human beings had not fully understood that dreams were not reality nor did they fully grasp the separation between animals/humans and the environment (known as "ego separation" to psychologists and anthropologists).
The latter development is significant because until human beings understood that we were not part of the environment but that we possessed free will entirely apart from the forces of nature, we were not capable of developing any sort of mature understanding of our possible relationship to a deity. IOW, until we understood who WE were as entities in the universe, we couldn't understand what a god was.
This latter development was likely not morphological (related to brain size) but rather a psychological development related to generational changes in how human mythology and awareness gathered information until a threshold of understanding of reality was achieved.
Sorry for the long exposition, but the topic is fascinating in relation to your idea - what sort of god has power over a mind that sees the universe differently from the way a modern human sees the universe.
