I vote for using the entire bypass. In my Avonds F-16 he specifically sez to not run the motor at high power setting without the top of the bypass to keep from collapsing the pipe. I dont want to experiment to find out if it matters. I personally think it will help the airplane with the bypass as the airflow will be cleaner through the motor vs the turbulence through the fuselage without it. I think they have lots of advantages for very little work.