You know, it didn't even occur to me until I read your remark that my story about being a young and naive car buyer might come across as "piling on" to criticize Honda. I don't think the auto maker had anything to do with it; I think this is just the typical sort of shady salesmanship that you see across the board at most or all dealerships for legacy auto makers, regardless of brand. This sort of shady dealing is why many EV advocates refer to them as "stealerships". I really didn't mean to single out Honda, and I loved my Civic CVCC, despite that early model having some build problems. I think Honda has a very good, well deserved reputation as an auto maker.
Be sure the fading you see on the black is not just dried up wax or shiner of some sort. I used wax on the black trim when I waxed the clarity and it eventually dried in the sun to look like that. If the dealer used some kind of shiner (like ArmorAll) to detail the car, it might look like that when it dried?
the scratches on the handle and the fading can be addressed by a detailer. Have you tried a car detail? They will remove light scratches and apply a sealant to the trims.
Hopefully you've got it all addressed. If the passenger door wasn't closing properly, it would not have automatically locked. That could cause a number of your problems. (I had a VW Passat that had a "hood open" sensor that broke shortly after I bought it; and it stopped beeping when locked.)