When crossconnect_factories is true, factories connection will be reconnected in finish_rd(). So, in my opinion, tool_link_factory_t (connect and remove factory connection tool) should be prohibited when crossconnect_factory is true.
In current version, we can remove factory connection with ctrl-key press even if crossconnect_factory is true. However, when we reload this map (e.g. save->load or Network mode reloading), this factories connection is reconnected.
OK, changed