I have an alabaster silver 2013 Civic Vti Oriel manual transmission as well and my advice to all people going or thinking of buying a manual is to not get it. Manual has next to no demand in the market and thus no resale. I bought mine just because I wanted to try out what a modern manual Civic would feel like because I had gotten rid of 1995 Civic which was manual as well and since then I had a longing to drive a manual. And one more thing, manual doesn't have any better fuel consumption than the automatic or at least in my experience it doesn't.
Any original service history is a plus point. Also check the airbags because most cars in the market have deployed airbags and there's a resistor that mechanics fix there to get rid of the light. Simply slide out the glove box and check underneath and observe if all the wires go into a medium size box. The airbag is just above a beam. Check the passenger side airbag cover for any creases that mighy seem too deep especially in the middle. The driver's side airbag cover shouldn't feel too soft becaue there's an airbag behind it which should make you feel some resistance when pressing the horn. Check if the driver side airbag lines up exactly with the back of the steering and doesn't stand out. If you see that there are open wires under the passenger side airbag, the airbag has been opened. Also check the seat belts; original Honda seatbelts have a stopper on them so the buckle doesn't fall below a certain height which is usually just below the headrest's height. Checking the airbags is crucial. Also check for any signs of new bolts or welds near and below the headlights as the front impact sensors are there and repair work is usually done in such areas when an airbag deploys.
Pakwheels carsure is utter shit. I went to check a few cars with the certification and believe me their reports said that the car had no scratches and no engine issues etc. The condition said 90 percent etc, but the car in reality was total junk. It didn't start because it had a fuel pump issue and would not accelerate properly. The "paint meter" they use to check the paint is some generic Chinese shit which is supposedly Polish (yes, Polish). It's on eBay for about 20 US Dollars and supposedly is as accurate as a 1k US Dollar Elcometer 311. The paint meter doesn't work on bumpers beause it has a magnet and the bumper is plastic. It's the Autolak BT 3003 for reference. You can get the report just for satisfaction purposes because sometimes people think "oh, I should've gotten the report and maybe I would've known of this earlier" etc.
Honda center does do a whole pre purchase inspection if you ask for it, at least in Islamabad. I asked the same question and was quoted 8k for it and considering the put the car up on a lift to check the underside for any frame damage, it's completely worth it because you're speeding more than 100 times than that on the car.
I have no idea of what the car is worth in Karachi, but I guess basic models are at least 1.5 lacs cheaper than the sunroof ones so you can work from there.