### 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
if (drop_events) {
		if (user_proc) {
			return CallWindowProcW(user_proc, hWnd, uMsg, wParam, lParam);
		} else {
			return DefWindowProcW(hWnd, uMsg, wParam, lParam);
		}
	}
	WindowID window_id = INVALID_WINDOW_ID;
	bool window_created = false;
	
	
	
	for (const KeyValue<WindowID, WindowData> &E : windows) {
		if (E.value.hWnd == hWnd) {
			window_id = E.key;