You are right, a duplicate SIM will stop the two-number method described from adding any protection.
But it will still protect against the fake messages like the ones being discussed here, and if someone has a duplicate SIM you are buggered in a number of other ways too.
Though this method, and several others that are effectively the same, only offers any protection if the user has the ware-with-all to bother verifying the other number. Unfortunately that means that in many cases it won't help at all because many would not be aware of the other number and expect to find it when the fake messages come in - unless the user knows to expect and require it the fact a fake message doesn't have it makes no difference.