3D models are present in the Materials section of Manga Studio. However, working with 3D models is so different from working with a 2D pattern that giving them their own chapters only seemed right. Having 3D models of figures and other objects available right in Manga Studio is a really useful thing! It makes getting reference for a difficult pose much easier. You don't have to scour the Internet, or get friends together for a photo shoot when you're on a deadline.
A good thing to remember though about using 3D elements in your work is that you should really use them as a reference, a jumping off point, instead of the be-all-and-end-all of the piece. Use a model to get the general pose that you want, then draw off of it. You really shouldn't throw a 3D model in with 2D artwork and leave it. It takes more work to make the combination of things looks good than is usually worth it. Most of the time 2D art with 3D elements stuck in just look awkward and strange...