HDR appears to be only JPEG while the Multiple Exposure Stacking is for RAW and JPEG.
"In-camera HDR shooting
In addition to the Multiple Imaging, the EOS 5D Mark III also features in-camera High Dynamic Range (HDR) shooting, thus allowing the creation of expanded dynamic range JPEG images. With HDR shooting, the camera will capture three images for each shot taken, with one being under-exposed, one correctly exposed and one over-exposed. These are then combined in-camera to create a single image.
When shooting HDR images, you can select the exposure range between the captured images or allow the camera to work it out automatically to suit the overall contrast. The manual range is between +/- 1 to 3EV. When the camera is processing the HDR images, there are several options on how the images are combined. These options range from Natural, which provides a natural looking result, to various creative effects like Art Standard, Art Vivid, Art Bold and Art Embossed."