### 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_double_click(true);
				} break;
				case WM_MBUTTONDBLCLK: {
					mb->set_pressed(true);
					mb->set_button_index(MouseButton::MIDDLE);
					mb->set_double_click(true);
				} break;
				case WM_MOUSEWHEEL: {
					mb->set_pressed(true);
					int motion = (short)HIWORD(wParam);
					if (!motion) {
						return 0;
					}
					if (motion > 0) {
						mb->set_button_index(MouseButton::WHEEL_UP);
					} else {
						mb->set_button_index(MouseButton::WHEEL_DOWN);
					}
					mb->set_factor(fabs((double)motion / (double)WHEEL_DELTA));
				} break;
				case WM_MOUSEHWHEEL: {
					mb->set_pressed(true);
					int motion = (short)HIWORD(wParam);
					if (!motion) {
						return 0;
					}
					if (motion < 0) {
						mb->set_button_index(MouseButton::WHEEL_LEFT);
					} else {
						mb->set_button_index(MouseButton::WHEEL_RIGHT);