The software not only decides how many images to bracket but what the bracketing parameters should be. The only setting that is set ahead of time is the amount of bracketing, 1/2 EV, 1/EV, 2EV, etc. The software then evaluates either the scene or the first image and then decides how many additional files to shoot and whether they should be over and/or under exposed.
When I was out this morning I intentionally looked for scenes with both high contrast and low contrast, lighting wise. The exposures ranged from two to six images and only one was the traditional over and under exposure in equal numbers. Some five frame brackets were the normally exposed image and then four underexposed images in one stop increments.
The files that resulted seemed to fit well with the "Balanced" presets in my HDR software, Photomatix Essentials 4.0. While the Magic Lantern software did choose six files for two of the scenes, the HDR software will only process five files so I deleted the darkest one.
I uploaded the twelve resulting images and the normally exposed files to a gallery on Zenfolio for anyone interested in examining them. The way I've set it up is explained in the Gallery description. The Gallery is located at http://trulandphoto.zenfolio.com/mlaeb.
One of the drawbacks of using the Magic Lantern bracketing is that is very deliberate in how it functions. While the built in Canon firmware lets you shoot at high speed continuous and stops when the bracketing is completed, Magic Lantern requires you to be in single shot mode and then evaluates and processes each file. Today, it was taking at least one second per shot whereas an EOS 70D, for example, can bracket five shots in less than a second. This could matter if the scene includes wildlife, clouds or people that are moving.
Here are a couple of examples. The first one is a five image HDR and the second a two image HDR.