I am from Karachi and studied in Lahore for 6 years for undergrad and then returned later for my masters.
From what I understand (i can't remember but i think this came from a guy who had good working knowledge of police procedures. I could be wrong since this conversation happened more than a couple of years ago) any FIR in Pakistan is linked to NIC number and the permanent address on the NIC. So what is needed is the PCC with your NIC and for the permanent address. So in your address history you should only write the permanent address since that is the one which is your permanent address.
So I did not need to furnish any PCC for Lahore. I only furnished one PCC for Karachi (which had my permanent address) and in my education history i clearly stated the years I was in Lahore (which overlapped with my PCC years obviously).
Everything turned out perfectly. I got my PR in 6 months, no issues.