You know that you can just put a ‘CustomFilter.plist’ file next to your .glyphs file (with the same format than the one from ‘Application Support/Glyphs’). You will get a second filter section in the sidebar. You can give the local group a name by adding it to the file name. So ‘CustomFilter My Secret Project.plist’ will be called ‘My Secret Project’.
Then the synchronisation with colleges is very easy as you can use the same ways as you sync the .glyphs file (e.g.: git or dropbox).
And I would strongly advise agains putting something in ~/GlyphsFilters. Those things belong in the App Support folder.