I'm pretty sure true C&C Mode is possible. The engine is highly moddable. However, the buildings would pop up at pre-determined locations when built for the sake of not screwing everything up (buildings inside of buildings, randomly placed buildings by n00bs, defenses in the enemy base, etc).
There are a couple of C&C fan-maps in UT2004 that have bases that build themselves when the player reaches a certain objective, and it unlocks higher technologies (vehicles and base defenses) when the structures are completed.