The emby user is a system user and it runs the application and is owner of the working directory. You just need to create a media share that is chmod has at least read for others. The media apps only need to read the files. After you created a media share you decide what user's that you've created have read/write or read privileges. Always try to use privileges and not acl.
This Native error = access denied thing is odd. It is like something we see when you are using a filesystem that does not work natively with linux. Can you give me a stat command on one of the files you are trying to play.
Can you tell me how some of the ffmpeg files are chmod 777 ??? Did you mess with their perms??