Thanks to a lot of work by myself and Darth Jane, its now possible to use PCCompression="EALAYER3" in the C&C3 Mod SDK and have it work and produce output that will work in the game.

To use it, you unzip the attached zip file into the "tools" folder underneath the main Mod SDK folder (making sure to overwrite the BinaryAssetBuilder.exe.config file) and then you create your mod as normal using PCCompression="EALAYER3" for anything you want to use the EALayer3 compression for.

This means you don't need the special AudioFileMP3Passthrough stuff anymore and can do things the way EA did it.

For those who are curious (and understand what they are doing) you can download the source code here:
https://github.com/jonwil/ealayer3compilerplugin 
https://github.com/jonwil/snrtool 
https://github.com/jonwil/lame-3.96 

If you have any questions about this, feel free to post here and I will do my best to answer them.   C&C3 EALayer3 Audio Plugin.zip (159kb) downloaded 72 time(s).

I fixed a bug in the plugin, it should now work properly.

  C&C3 EALayer3 Audio Plugin.zip (162kb) downloaded 60 time(s).

I finally sorted some further bugs in the plugin and now it should actually work correctly.

  C&C3 EALayer3 Audio Plugin.zip (161kb) downloaded 58 time(s).

I unzipped and made the mod as instructed, awesome!
slope game