The main reason is money (on both sides).
For the rights holders, they want to milk these movies until the end of time. What better way to make sure they get their money's worth than to make sure people can't import these titles. The rights holders want the potential customers to wait until a label from their designated territory picks up the film (thus paying them big money). If they let people use region free encoding, they would not sign many contracts with labels.
For companies like myself, why would we release a title if it is already able to be imported? If there was a region free release of PER UNA BARA PIENA DI DOLLARI, I would most likely avoid releasing it -- as a good portion of fans would have likely imported it. In this case though, we have plenty of features to rival Koch and whoever else might have put this out. But this isn't the case for all films.
That being said, some companies do not enforce a region lock on their catalog titles -- although it's quite rare.