### 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
_THREAD_SAFE_METHOD_
	ERR_FAIL_COND(!windows.has(p_window));
	WindowData &wd = windows[p_window];
	XStoreName(x11_display, wd.x11_window, p_title.utf8().get_data());
	Atom _net_wm_name = XInternAtom(x11_display, "_NET_WM_NAME", false);
	Atom utf8_string = XInternAtom(x11_display, "UTF8_STRING", false);
	if (_net_wm_name != None && utf8_string != None) {
		XChangeProperty(x11_display, wd.x11_window, _net_wm_name, utf8_string, 8, PropModeReplace, (unsigned char *)p_title.utf8().get_data(), p_title.utf8().length());
	}
}
void DisplayServerX11::window_set_mouse_passthrough(const Vector<Vector2> &p_region, WindowID p_window) {
	_THREAD_SAFE_METHOD_
	ERR_FAIL_COND(!windows.has(p_window));
	windows[p_window].mpath = p_region;
	_update_window_mouse_passthrough(p_window);
}
void DisplayServerX11::_update_window_mouse_passthrough(WindowID p_window) {