I saw some time ago on the Joplin github that they might add the option of saving the notes in markdown somehow, but not sure that’s implemented or even progressing.

Have you tried QOwnNotes? I haven’t used it but I’ve seen it, looks like it ticks everything you want.

I would also highly recommend logseq, org-roam, or vimwiki. For mobile support, definitely use syncthing (logseq has a paid sync feature, but it’s not worth it over self-hosting syncthing imo. It’s easier technically speaking, but syncthing is pretty easy too)

Logseq - I use this now, primarily because the mobile app is as great as the desktop version. Links, tasks, etc are all smooth and I love the workflow. Only reason I don’t think you’d like it is you can’t really have your own defined dir structure.

Org-roam - uses .org files that have their own syntax and such, also foss and non-proprietary though. I used it for a while because the emacs ecosystem is very robust and I use emacs a lot. Primary downside to this system is mobile support hurts, I used OrgNote for a while but just didn’t like it much. (If you go this route, highly recommend using doom emacs instead of just vanilla. Vim keybinds are the best keybinds)

Vimwiki - uses vim keybinds, love it. Same issue as org-roam though, mobile support makes me cry. There are plenty of foss mobile md editors, but none of them feel good. You can use this as a wiki via GitHub and have access to it from any web browser and make edits there as well, but it wasn’t a very pleasant workflow personally.