I usually have “blank” arrangement sections that I put at the beginning and end of my arrangement. That gives me those parts at the top or end if I need to throw clips, etc, in to those areas so that the flatten doesn’t get rid of them.
For me it’s faster to just open the bounced stereo wave in a new project and do final fades to get the length exact. You can even just have Cubase open the finished bounce in a new project automatically.