Dunno what permissions issues you’re hitting, but I organize everything with beets on my desktop and then sync everything using syncthing to the main Music folder on my phone and it all works nicely. I use an old app that I think isn’t even available on the app store anymore named MortPlayer that uses the synced folder structure to organize things.
I don’t use m3u files, but I imagine you could just sync them to the main Music directory next to the music files and have it work out, I guess depending on which app you use