### 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
}
			Ref<InputEventMouseMotion> mm;
			mm.instantiate();
			mm->set_window_id(window_id);
			if (pen_info.penMask & PEN_MASK_PRESSURE) {
				mm->set_pressure((float)pen_info.pressure / 1024);
			} else {
				mm->set_pressure((HIWORD(wParam) & POINTER_MESSAGE_FLAG_FIRSTBUTTON) ? 1.0f : 0.0f);
			}
			if ((pen_info.penMask & PEN_MASK_TILT_X) && (pen_info.penMask & PEN_MASK_TILT_Y)) {
				mm->set_tilt(Vector2((float)pen_info.tiltX / 90, (float)pen_info.tiltY / 90));
			}
			mm->set_pen_inverted(pen_info.penFlags & (PEN_FLAG_INVERTED | PEN_FLAG_ERASER));
			mm->set_ctrl_pressed(GetKeyState(VK_CONTROL) < 0);
			mm->set_shift_pressed(GetKeyState(VK_SHIFT) < 0);
			mm->set_alt_pressed(alt_mem);
			mm->set_button_mask(last_button_state);
			POINT coords; 
			coords.x = GET_X_LPARAM(lParam);
			coords.y = GET_Y_LPARAM(lParam);
			ScreenToClient(windows[window_id].hWnd, &coords);
			mm->set_position(Vector2(coords.x, coords.y));
			mm->set_global_position(Vector2(coords.x, coords.y));
			if (mouse_mode == MOUSE_MODE_CAPTURED) {
				Point2i c(windows[window_id].width / 2, windows[window_id].height / 2);
				old_x = c.x;
				old_y = c.y;
				if (mm->get_position() == c) {
					center = c;
					return 0;