Exporting cameras from one program to the other seems to be pretty easy, and makes working with the PNG sequences not as limiting as you may think. Lets say you have a camera move in 3ds or any other program, with your model (lets assume the fighter jet from the tutorial). You render out the animation with an alpha channel. Then export the 3d camera for After Effects. Bring it in to After Effects, and you have a 3d camera that mimics the exact moves from the camera in 3ds. You now have your PNG sequence, but this is left as a 2d layer. Anything that is made a 3d layer will move as they should with the perspective given by the 2d layer. You can easily composite skies, elements, whatever you may want.
After all, AE is a compositer first, with some incredibly awesome capabilities. The drawback is that it doesn't do true 3d geometery out of the box, and even with plugins it's limited. With a 3d program and After Effects combines, however, that's power.
