Creative Cloud Auto Update: Transfer Render Settings and Output Modules

If you migrate your preferences with the GUI once, then I believe they should be available to aender. Are you saying that you open the AE UI, migrate preferences, can see the Render Settings and Output Modules have migrated and show up in your Render Queue, but they still aren't available via aerender?

But either way, here are the location of your preferences:

• Windows: \Users\[user_name]\AppData\Roaming\Adobe\After Effects\[version]
• macOS: /Users/[user_name]/Library/Preferences/Adobe/After Effects/[version]

Inside the folder of the version you want to migrate from, there will be two files that hold your Render Settings and Output modules. Copying those to your current version and renaming the file name to include the version number should do the trick. 
Adobe After Effects [version] Prefs-indep-output.txt

Adobe After Effects [version] Prefs-indep-render.txt

Thanks,
- David, After Effects Engineering Team