### 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
Input::get_singleton()->parse_input_event(mm);
		} break;
		case WM_LBUTTONDOWN:
		case WM_LBUTTONUP:
			if (Input::get_singleton()->is_emulating_mouse_from_touch()) {
				
				LPARAM extra = GetMessageExtraInfo();
				if (IsTouchEvent(extra)) {
					break;
				}
			}
			[[fallthrough]];
		case WM_MBUTTONDOWN:
		case WM_MBUTTONUP:
		case WM_RBUTTONDOWN:
		case WM_RBUTTONUP:
		case WM_MOUSEWHEEL:
		case WM_MOUSEHWHEEL:
		case WM_LBUTTONDBLCLK:
		case WM_MBUTTONDBLCLK:
		case WM_RBUTTONDBLCLK:
		case WM_XBUTTONDBLCLK:
		case WM_XBUTTONDOWN:
		case WM_XBUTTONUP: {
			Ref<InputEventMouseButton> mb;
			mb.instantiate();
			mb->set_window_id(window_id);
			switch (uMsg) {
				case WM_LBUTTONDOWN: {
					mb->set_pressed(true);