Could be he used the intake pipe nipple to prime the engine and the other end was on the close nipple to seal the system, you'll want to close off that nipple somehow,, yes
The only reason I can imagine for the closed off nipple was for could be the guy moved the muffler pleasure line to that to prevent fuel other from spilling out the tank when working on and or transporting the plane. When you have a plane that needs to be upside down to mount/remove the wing, a little fuel dribbling can be an issue.
Good luck