@omar_575 congrats on the new car! Very interesting to read your detailed review in this post. I also have a 9th gen/2013 civic (mine's black) and wanted to add a few things:
1) I had the boot closing issue too (it's apparently so common that I wonder if it comes as a 'feature') However the Honda center guy here in Isb took <5 minutes to fix it by tightening/loosening some nuts. I'd say, best to get it fixed from them rather than trying anything at home.
2) A major, MAJOR gripe I have with the car is the gear shifting (mine's an automatic tranny). The shifting feels jerky and just sad on lower gears especially. My other auto experience has been with a City Steermatic 1.5, and I don't think I ever felt a gear change in that car. So much so that I thought there was something wrong with the Civic, and had it inspected by Honda techies, but they said 'this is normal since the Civic does not have CVT, because logon ne CNG lagwani hoti hai na, so it has a progressive shift system that supports CNG better'. utter disbelief People who've driven a CVT may feel the difference more.
3) After ~3k km, I'm getting between 8.5-9 ish within city (Isb/Rwp) with a light-ish foot and economy mode, but much better on the motorway with cruise control.
4) I've been pointing out the 'orange peel' issue with the paint on other threads also, and even wrote to Honda Atlas about it. Khair, I've seen over time that there are some very skilled and very helpful members here, and with their help one can make do quite nicely with this nonetheless. For example I would strongly recommend any advice from my virtual ustaad @ahmad_yar bhai, who's been helping a detailing/car-care noob like me going out of his way
A clarification: This is not to say I am unhappy with the car all in all. Alhamdolillah
All the best!