For example, I've experienced that if you don't place certain buildings but you do place the units that require them the AI will build the structures on its own (e.g. Ghost Academy, Fusion Core). I've experience with Terran AI from my RTC map, so I know what I'm talking about.
For customization I mean even what you said. Make an AI build/rebuild what you want is a simple way to customize it. Co-op AI will do certain things no matter you, also depending on the difficulty.
Now, I wonder, why should not your AI build those structures? What do you want your co-op AI to do?
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Battle.net wants to call me InsaneMst, Insane... but you should call me InsaneMonster!