How to render out JUST Alpha in Media Encoder

So apparently Adobe has changed their settings in CC 2014 and Adobe After Effects no longer has the H.264 container, and is only offered as a codec for Qucktime. I've been told I have to go into Adobe Media Encoder for the H.264 codec. That's fine, problem is that Adobe Media Encoder does not really have any options for Alpha. From my understanding you have to set it to 32bpc for it to do alpha in a file, which did not seem to work, but that's irrelevant now because that's not what I need. I need to render out two files for a batch list, one with just RGB files and one with just alpha. I talked to someone from Adobe and they suggested I post here. Let me know if you need details.
Thank you very much.

Just to be clear, and reiterate what Kevin state: H.264 (.mp4) files do not have the capability of storing an alpha channel. They are RGB only.
But that doesn't sound like a blocking issue for your workflow; you're already preparing to use an RGB file and a separate file with a black/white alpha matte for compositing at playback time.
Another point to make clear: the controls in the Composition viewer panel in After Effects have no affect on the rendered output. AME will read the comp as if these controls don't exist. Even the After Effects render queue by default will ignore these settings, though you can change some of the controls in the Render Settings dialog to respect the Comp viewer settings (ie., Current Settings). AME doesn't have this capability for After Effects comps, currently.
Third point: AME doesn't have the capability to produce an alpha-channel-only video, like After Effects does. This is regardless of what type of source you're using, After Effects comp, Premiere Pro sequence, or other.
Fourth point: please submit a feature request for any functionality you'd like to see added to AME, or After Effects: http://adobe.ly/feature_request
For your workflow the best thing will probably be to do what Jeff recommends: have After Effects render your comp to two Output Modules, one with RGB and one with Alpha, in a lossless format and then have AME encode the files to your final delivery format. This can be automated with watch folders.

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