### 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
LPARAM extra = GetMessageExtraInfo();
				if (IsTouchEvent(extra)) {
					break;
				}
			}
			DisplayServer::WindowID over_id = get_window_at_screen_position(mouse_get_position());
			if (windows.has(over_id) && !Rect2(window_get_position(over_id), Point2(windows[over_id].width, windows[over_id].height)).has_point(mouse_get_position())) {
				
				over_id = INVALID_WINDOW_ID;
			}
			if (window_mouseover_id != over_id) {
				
				if (mouse_mode != MOUSE_MODE_CAPTURED) {
					if (window_mouseover_id != INVALID_WINDOW_ID && windows.has(window_mouseover_id)) {
						
						_send_window_event(windows[window_mouseover_id], WINDOW_EVENT_MOUSE_EXIT);
					}
					if (over_id != INVALID_WINDOW_ID && windows.has(over_id)) {
						_send_window_event(windows[over_id], WINDOW_EVENT_MOUSE_ENTER);
					}
				}
				CursorShape c = cursor_shape;
				cursor_shape = CURSOR_MAX;
				cursor_set_shape(c);
				window_mouseover_id = over_id;
				
				track_mouse_leave_event(hWnd);
			}
			
			if (!windows[window_id].window_has_focus && mouse_mode == MOUSE_MODE_CAPTURED) {