Buddy i am a son of an army officer and we moved around quite a lot. we have settled in Karachi and i own two cars non-karachi registered one is lahore and the other one is islamabad reg. There are no worries as to the runing the car legally on the road but a few thing to take notice of are:
1) Dont use fancy no. plates which are very common n punjab but might be a headache in karachi. Use the original plates or an exact replica.
2) you might have an issue with the resale of the car. if you are planning to keep this car for the length of your stay over here then its fine otherwise sell it off over there and get an evenly priced car from here.
3) my opinion is that its actually safer to have a non-karachi registered car in karachi cuz it makes the car easy to spot if God forbid sombedy steals it or attempts to steal it. But thats just my personal opinion. More importantly you have to know which areas are safe and which arent.
4) get your car anti-rust treatment from your dealer that might save your car.
I guess thats it. Happy driving in Karachi!