Donohue said in his book it was to let hot air our from under the hood, and to help cool the rear tires. The downforce theory is interesting. Air trapped beneath the hood probably would have had the effect of lifting the nose at high speeds, but my limited understanding is that the front chin spoiler plus hood cowl scoop would have helped both press the nose into the ground and release trapped air. Maybe the concept of the ducting system was also to release air as well as engine bay heat.
The Penske team were originally planning to fit front tires to their '69 cars that were at least as big as the back tires, hence the heavily flared fenders. But in testing they couldn't get the cars to handle right, so reverted back to smaller front tires.