Ubuntu – How to remove the application’s appindicator programmatically

Unfortunately, appindicator doesn't allow adding custom widget, as it requires GObject introspection. This will be available when ido package will have GObject instrospection.

Bug report

Application indicators are based on KStatusNotifierItem.

I'm not too familiar with it but here's a tutorial on how to get started. That's all you really need to get it to work, the app icon and it's menus should then render properly regardless of which desktop it's in.