3D sources means their graphics are built in 3D (using models and textures and so forth) and then they render to 2D (with extremely high-quality settings obviously, since this only has to be done once), and then the rendering is saved as a flat image. In much the same way as how you have a 2D image on your monitor at any given moment while playing a fully 3D game, and you could just save off that image if you wanted. And then bring it up in an image viewer at any time you wanted, without having to re-render the 3D. However, it was still generated from 3D graphics techniques originally, and not hand-painted.
Among other things, some reasons to do that would be to (1) eliminate any performance issues at play time, because your video card doesn't have to do 3D rendering of any of the background (and especially not at the extreme settings they would have used), and (2) allow for hand-touchups.