In my mod I have been using the "NoMoreThanOne" flag trick to prevent more than on module of a given type to be included in a ship design. Problem is, when a newer version of the module is available, the auto-upgrade feature don't work for it. It would be nice if the auto-upgrade worked for those, or that a better way of limiting modules per ships be included in the game (like being able to define how many of each modules are allowed).