If when you're setting up an AI empire to play
against you allow it to access one of the other
research tree's (eg. Organic)as a bonus will it
take advantage of this "bonus" if the AI files
don't research this field?
No, it will not. The AI has to be programmed to research the new technologies made available, as well as to be able to use the new items (facilities, components, etc.) that they allow.