Glass containers work great for food that has liquid as a major component. (Flan is awesome!) Think of doing canning except it's really cooking for immediate use rather than for long term preservation and the food can take the shape of the container. A plastic container can conform to the shape of the food. Each has a place in Sous Vide.
Also don't get hung-up in the "vacuum" thing. We're really just evacuating the air/gasses to ensure even cooking. The process uses a vacuum but the actual vacuum is unimportant.