sorry for the delay in answering, it's been some crazy months lately.
I think we've never had issues with Apple because of those things, but it's true that some reviews are more strict than others depending on the reviewer. Sometimes they complain about things that've been published for months!
That plugin was added because some institutions use audios as lectures and they need them to be played while the app is in background. If that's not your case then you can just remove the plugin as you did. If you need the feature, then you should tell Apple why do you need it and add at least one embedded audio to your course so they can test it.