### 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
}
					mb->set_factor(fabs((double)motion / (double)WHEEL_DELTA));
				} break;
				case WM_XBUTTONDOWN: {
					mb->set_pressed(true);
					if (HIWORD(wParam) == XBUTTON1) {
						mb->set_button_index(MouseButton::MB_XBUTTON1);
					} else {
						mb->set_button_index(MouseButton::MB_XBUTTON2);
					}
				} break;
				case WM_XBUTTONUP: {
					mb->set_pressed(false);
					if (HIWORD(wParam) == XBUTTON1) {
						mb->set_button_index(MouseButton::MB_XBUTTON1);
					} else {
						mb->set_button_index(MouseButton::MB_XBUTTON2);
					}
				} break;
				case WM_XBUTTONDBLCLK: {
					mb->set_pressed(true);
					if (HIWORD(wParam) == XBUTTON1) {
						mb->set_button_index(MouseButton::MB_XBUTTON1);
					} else {
						mb->set_button_index(MouseButton::MB_XBUTTON2);
					}
					mb->set_double_click(true);
				} break;
				default: {
					return 0;