I’m with you, packaging is broken in UE4. It’s fine for anything that’s referenced; anything else isn’t included.
You can see that simply by looking at the command line the editor passes to UAT (it starts with BuildCookRun) when you start packaging your project. It won’t pass along any extra directories specified in the .ini file.
The only workaround I have is to have a build script that removes content I don’t want packaged and then to specify that I want it to package all content (which uses the argument -CookAll). I’ve looked through the parameters supported by UAT and I can’t see one that would cook and/or package other content.