There is no real way to do that in Wayland as of yet. The flag does nothing with the Wayland GTK backend, but also Mutter seems to lack the code to do it. Maybe some other compositors have another custom Wayland extension that supports it, if they did it would have to be added to GTK. You could put in a feature request, but I would say you just want to completely avoid doing that on Wayland. It is a bad idea. Stretching a single buffer across all monitors won’t work right when the displays have different refresh rates.
It seems likely that running the application as root is causing it to fall back to Xwayland which still preserves the old X11 behavior. You could try to test with a GDK_BACKEND=x11 environment variable to see if it also works that way.
You can implement in your application using several windows that each pull from an offscreen buffer. This is technically what the wayland compositor would be doing anyway.
Otherwise, you would have to put in a feature request for a new Wayland extension that can fullscreen a window using a list of outputs. I don’t think that exists yet.