### Godot version

4.0.beta12

### System information

Windows 11, RTX 3080

### Issue description

When a Window Node is created with it's Transparent flag set to true and Project Settings --> Display --> Window --> Subwindows --> Embed Subwindows is false, the Window has a black background. By cycling the transparent flag from false and back to true again, during runtime, the window's background then becomes transparent. 

### Steps to reproduce

Attempt to create a Non-embedded Subwindow with a transparent background using the appropriate flags. 

### Minimal reproduction project

Note: this project is from Reddit user [gongpha](https://www.reddit.com/user/gongpha/) and his Reddit post [Learning a Godot 4.0 Window node](https://www.reddit.com/r/godot/comments/xr8yxn/learning_a_godot_40_window_node/)

https://github.com/gongpha/godot4-window-test
_THREAD_SAFE_METHOD_
	List<WindowID>::Element *E = popup_list.find(p_window);
	while (E) {
		List<WindowID>::Element *F = E->next();
		WindowID win_id = E->get();
		popup_list.erase(E);
		if (win_id != p_window) {
			
			_send_window_event(windows[win_id], DisplayServerWindows::WINDOW_EVENT_CLOSE_REQUEST);
		}
		E = F;
	}
}
LRESULT DisplayServerWindows::MouseProc(int code, WPARAM wParam, LPARAM lParam) {
	_THREAD_SAFE_METHOD_
	uint64_t delta = OS::get_singleton()->get_ticks_msec() - time_since_popup;
	if (delta > 250) {
		switch (wParam) {
			case WM_NCLBUTTONDOWN:
			case WM_NCRBUTTONDOWN:
			case WM_NCMBUTTONDOWN:
			case WM_LBUTTONDOWN:
			case WM_RBUTTONDOWN: