I'm Selfhosting Jellyfin (navidrome too, but I think I like Jellyfin more), so it's all central on my homeserver.

What I do is have a separate /synced/media/music folder on both my pc and phone, and use syncthing for that and don't worry about the default Android music folder.

For playlists I do that on my pc with the music player Strawberry, I can add songs to a playlist and save it as a .m3u file in that same /synced/media/music folder. The playlists still work on my phone since it's just local paths from the root of my music folder. I would do playlists on my phone as well but I use JetAudio which is pretty buggy and doesn't let me modify .m3u playlists, although I'm sure some other player would let you create and modify them.

Umm... I don't. I use CMUS which uses its own playlist structure, and on top of all that, I make changes to my music collection on my phone that I am yet to sync over to my Linux machine and then to a USB which acts as a backup solution. I know that in the sysadmin realm they say "2 is 1, 1 is none", but that usually goes for untested backups, or backups that can be lost in various ways. Personally, if I have my music collection (or at least most of it on 3 different devices most of the time and on at least 2 devices at 100% of the time (when I'm tinkering with my phone or distrohopping), I'd say I'm pretty safe.

I only use like three playlists so I wrote a script to make .m3u playlists with those artists but it's not perfect cause it pulls the data from the file path and not the metadata

I am now realizing this isn't very helpful but I copy only a bit of music from my hard drive to my phone cause limited space so the scripts keep the playlists the same mostly

Edit: I just realized this asked about syncing. Oops. I guess I sync by copying music to my phone and then pointing the scripts to read the music folder there instead of the hard drive but I realize now that might not be what you want

I'm Selfhosting Jellyfin (navidrome too, but I think I like Jellyfin more), so it's all central on my homeserver.

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