Mulit city does not effect this. Airlines put this policy in place to prevent people from booking a round trip or multi city ticket at a lower price than a higher priced direct flight and then only use certain segments.

There are many times when a flight originating in a non hub city is much cheaper than a the hub to destination flight. So to prevent people from booking the non hub city flight when they only really wanted the flight from the hub does not work, as the connection will be cancelled if the first flight is missed.