### Godot version

Master (0ddd9c3e8f9088fa139e25b2903289d727073e12)

### System information

PopOS 22.04 - Intel integrated graphics - all backends

### Issue description

When there are popup windows in the editor, I cannot click on the "Confirm"/"Cancel" type buttons at the button. 

I have the issue both in the project manager (importing projects I can click on files etc. but cannot click "open") and when running the editor (cannot click "Save&Quit" etc.)

Sometimes the editor correctly highlights the buttons and I can use the arrow keys to navigate the buttons and "enter" to confirm my selection.

_I can navigate the editor closing dialogue with tab/arrow keys_
![Screenshot from 2023-01-16 14-24-06](https://user-images.githubusercontent.com/16521339/212774269-d784ea5e-5921-4460-9124-48978939c8e7.png)

_I can't navigate the project import dialogue with tab/arrow keys_
![Screenshot from 2023-01-16 14-29-00](https://user-images.githubusercontent.com/16521339/212774683-0a80795a-eed4-4e65-b2ca-3562c25d71fd.png)


### Steps to reproduce

Run the editor

### Minimal reproduction project

Reproducible in the project manager
ERR_FAIL_COND_V(!windows.has(p_window), 0);
	switch (p_handle_type) {
		case DISPLAY_HANDLE: {
			return (int64_t)x11_display;
		}
		case WINDOW_HANDLE: {
			return (int64_t)windows[p_window].x11_window;
		}
		case WINDOW_VIEW: {
			return 0; 
		}
#ifdef GLES3_ENABLED
		case OPENGL_CONTEXT: {
			if (gl_manager) {
				return (int64_t)gl_manager->get_glx_context(p_window);
			}
			return 0;
		}
#endif
		default: {
			return 0;
		}
	}
}
void DisplayServerX11::window_attach_instance_id(ObjectID p_instance, WindowID p_window) {
	ERR_FAIL_COND(!windows.has(p_window));
	WindowData &wd = windows[p_window];
	wd.instance_id = p_instance;
}
ObjectID DisplayServerX11::window_get_attached_instance_id(WindowID p_window) const {