How to export a After Effects video in Media Encoder as a transparent MP4 video instead of MOV

If a client requests an MP4 with transparency, they do not understand video formats and should be gently educated.

The MP4 format only supports RGB and usually compresses color (averages) in a 2:1 or a 4:1 ratio. It also usually interprets the movement of details in 3 out of 4 frames. It's a horrible choice for a production master. 

The only option is to render the MP4 and then Render it again, choosing Alpha Channel Only to generate a high-contrast black-and-white copy. Then, you must deliver two files: one black-and-white showing the transparency and one in color.

The easiest option for one file would be to use the High Quality with Alpha preset in the Render Queue's Output Module settings. 

See here:

https://community.adobe.com/t5/after-effects-discussions/how-to-export-mp4-media-encoder-with-a-transparent-background/td-p/10073445