It should be possible to just use two fields in the GUI for Local Ignore (the current one) and a Global Ignore (the new second). This would then be followed by two files, one of which is copied between the connected devices. That would certainly be a representable standard. Multiple #include entries would then be used for a multi-global ignore environment.
Since more and more system files are added, maybe again we take up the systemic Syncthing subdirectory again.