Correct, but a third baffle will reduce bubbles. As the water rushes down the first baffle and then under the second, a certain percentage of the bubbles will make it under the second baffle and are exposed to the pump.
If you pump intake is far enough away from the baffles, you will probably have no micro-bubbles. However, if that is not possible, or the bubbles still find their way to the intake, a third baffle will give the bubbles a chance to rise and pop before entering the return section.
However, to FishTV's point, if the water level in the return pump area is too low, then the water will "crash" into the return section from the third baffle and create new bubbles. Actually - this is a good indicator for you. If you start to see micro-bubbles or (in my case) hear the cascade of the water, you can be sure that your ATO is probably not functioning as expected. Mine can cascade about 2 inches before it becomes an issue. Mileage will vary based on depth, etc...