Yes there has definitely been system tray issues in windows 11. There are various "workarounds" that don't seem to do anything such as deleting the icon cache and a couple of registry entries. Also, if your explorer.exe crashes and restarts you may lose icons in the system tray.
However, I think Windows 11 has become more stable in this area. I can't say exactly at what point. But I think even at 23H2 it was stable.
Thank for for forwarding the issue. I found this one curious in that you can get the system tray icon by just toggling the setting off and on in deskscapes. But unfortunately it will not persist across boots.