It seems like the the people making the film were happy to work with the foundation, for whom this was their first such request.

Even if they had an adversarial posture towards the foundation, the alternative would probably involve a court of law sorting this out, with all the costs of time and money that entails. Even if they were certain they were in their rights to just add a watermark, any risk that could potentially render the film unreleasable for an any amount of time would be unacceptable.