I just went through this process and it's the same old rubbish (police fir, news paper report fingerprints etc) and a month later I got my card with duplicate printed on the back.
I personally don't think the problem is with the system, it's more a perception, people have had bad experiences in the past with police giving them a lot of trouble with duplicate books, i don't see that as a huge issue these days with the smart cards, it's impossible to do anything in Pakistan these days without giving fingerprints and buying selling car is no exception.
Another thing to note is that a buyer will try all sorts of tricks to bring price down.l, and you bet duplicate card is going to be one of them.