After Effects only recognizes the primary alpha channel, and I don't think it's a matter of what it's named as much as if there is an additional channel.
However, there are ways of applying data from two alpha channels provided you render them separately.
You can bring in your clip with the basic alpha channel for transparency. And then you can import the z-depth alpha render and use it as an alpha matte to the imported video. This will then enable you to apply effects like fog, blur, color correction, etc. to the video track using the z-depth information.
I frequently use this approach as I have the capacity to output z-depth as a greyscale sequence from applications like Vue Infinite, so that I have just the "alpha" information to use with the rendered video plates. Of course in that instance, I would use luma matte instead of the alpha matte because I'm using the greyscale values of the z-depth render itself, and not the z-depth information that is embedded in an alpha channel of a second video clip. If Maya will render the z-depth out as a greyscale sequence (I would think it should), you can do the same thing, and have less file overhead for the same effect.