In general, and this applies to every camera from the cheapest cameraphone to the most expensive SLR, "auto" means "do what the camera thinks is best for the given scenario". While certain cameras may fix some "auto" parameters under some circumstances (for example, I know that my Canon SLR fixes ISO at 400 if the flash is in use), the general case is that "auto" parameters are variable.
One thing to note here is that you don't actually have three variables to modify, as the physical characteristics of the photo are defined by the shutter speed and ISO; this is the exposure triangle, except that things are a simpler on cameraphones where the lens has a fixed aperture. So what does "brightness" do? Well, in the situation where you've got either the shutter speed or ISO set to "auto", the camera will be making a guess as to how bright it thinks the scene should be - and the "brightness" control lets you modify that guess. In the situation where you've set a specific value for both shutter speed and ISO, I'd imagine that the "brightness" control is disabled as it has no parameters left to modify.