If we get the ability to edit the tech tree that much, clearly the AIs can't possibly be expected to properly use custom tech trees. We're going to need an AI editor to design AIs, just for that.
The AI in GalCiv is not like AIs in other games. It will adapt automatically to custom tech trees.
The AI doesn't know anything about the tech trees in Dark Avatar. It has no hard coded paths to take.
It does look at the AI value to help pick when it has to make a blind pick. But otherwise, it uses the categories and branches (which are defined) to make intelligent choices.
Any decently made custom tech tree will adhere to calling manufacturing technologies manufacturing (as opposed to say cultural).
As for the argument as to why Micro Fusion was invented by humans - it has to do with intertia. Why did some groups of humans remain hunter/gatherers while others invented rockets.
For 30,000 years, humans basically hung out in the jungle and in caves.
The premise of the Arcean and Drengin is that their worlds, long united, fell into a kind of technological inertia. There was little incentive to move forward with technology.
Incidentally, the technology in the Star Wars universe doesn't really change either. It's a common theme in both the real world and in fiction that some societies simply peak and then stay the same unless there is outside influence.