Export alpha channel directly as a mp4 format?

Mp4 files cannot contain an alpha channel.  But you can output the alpha channel as a standalone file.

When you're ready to render, add your comp to the Render Queue from Composition > Add to render Queue.

Click on the Output Module in the Render Queue, and make sure it is set to RGB.

Then, with Output Module selected, click on Composition > Add Output Module.

This will add a second output to your Render Queue item.  Click on the second output module, and change the Channels setting to Alpha.

Set the output file name.  Now, when you render, you'll create two files simultaneously - the Fill layer, and the alpha channel, as seperate files.

You can set the render options to Alpha only on the AE render queueu and nothing stops you from setting two consecutive renders of the same comp with different options, so I fail to see your problem, especially given that the second render usually would be a lot faster with AE having already cached a considerable part of the frames. Otherwise there is no way to do it with MP4s, no matter how you twist and turn it. You can't expect AE to do what an output format doesn't support and in fact pretty much the only format that would allow a workflow as you seem to envision would have been the old Quicktime Animation CoDec, which had an Alpha only option natively (along with other useful stuff).

Mylenium