i had my father's 9th gen civic fixed from city sales. all they is close the console with folded tissues pressed between the lock, and they noise is gone.. i didn't get the logic, but its all okay now.
the misaligned trunk problem is due to the position of the trunk lock. have it checked properly. i had the same problem (misaligned trunk) in my father's car, the mechanic straightened the hook and had it tightly screwed, the trunk closing problem and the misaligned problem is gone.