### 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_ctrl_pressed((wParam & MK_CONTROL) != 0);
			mb->set_shift_pressed((wParam & MK_SHIFT) != 0);
			mb->set_alt_pressed(alt_mem);
			
			if (mb->is_pressed()) {
				last_button_state.set_flag(mouse_button_to_mask(mb->get_button_index()));
			} else {
				last_button_state.clear_flag(mouse_button_to_mask(mb->get_button_index()));
			}
			mb->set_button_mask(last_button_state);
			mb->set_position(Vector2(GET_X_LPARAM(lParam), GET_Y_LPARAM(lParam)));
			if (mouse_mode == MOUSE_MODE_CAPTURED && !use_raw_input) {
				mb->set_position(Vector2(old_x, old_y));
			}
			if (uMsg != WM_MOUSEWHEEL && uMsg != WM_MOUSEHWHEEL) {
				if (mb->is_pressed()) {
					if (++pressrc > 0 && mouse_mode != MOUSE_MODE_CAPTURED) {
						SetCapture(hWnd);
					}
				} else {
					if (--pressrc <= 0) {
						if (mouse_mode != MOUSE_MODE_CAPTURED) {
							ReleaseCapture();
						}
						pressrc = 0;
					}
				}
			} else {