### 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
}
						Point2i ncenter = mm->get_position();
						center = ncenter;
						POINT pos = { (int)c.x, (int)c.y };
						ClientToScreen(windows[window_id].hWnd, &pos);
						SetCursorPos(pos.x, pos.y);
					}
					mm->set_velocity(Input::get_singleton()->get_last_mouse_velocity());
					if (old_invalid) {
						old_x = mm->get_position().x;
						old_y = mm->get_position().y;
						old_invalid = false;
					}
					mm->set_relative(Vector2(mm->get_position() - Vector2(old_x, old_y)));
					old_x = mm->get_position().x;
					old_y = mm->get_position().y;
					if (windows[window_id].window_has_focus || window_get_active_popup() == window_id) {
						Input::get_singleton()->parse_input_event(mm);
					}
				}
				return 0;
			}
		} break;
		case WM_POINTERENTER: {
			if (mouse_mode == MOUSE_MODE_CAPTURED && use_raw_input) {
				break;
			}
			if ((tablet_get_current_driver() != "winink") || !winink_available) {
				break;
			}