The menu is not Scintilla so its not unexpected that it doesn't affect it.
No Geany devs use Wayland AFAIK so perhaps you could try replacing [this call](https://github.com/geany/geany/blob/5d4e7cfd5b12647b4cab9bda7278abd7f63e9c2f...) with a call to [this](https://docs.gtk.org/gtk3/method.Menu.popup_at_pointer.html) and see what happens.