The AI Zones are as he said, to direct the AI to not fly over high mountains and walk under water.
The Passible Zones are mainly for you the Human payer from traversing Mountains and Walking under water for example.
Ther are other pathing option to help the AI 'know' the routes to your main bases. Or you can just rely on the AI default scripts -which are bit dense to find you.
And the retreat/defensive marker is good to tell the AI where to run to and hide if getting a beating, such as go hide under a well defened bast shield. They are areas on the map where you would go.