OK, that I can see. The silver washer thing below the silver tapered section in there is a preload spring, also known as a wavy washer. That will not sit flush. Its purpose is to keep the crank from moving loosely left to right - prevent axial play.
The black ring below that is a cap that hides the interior. It is not a seal and needn't be flush, although from this photo it is nice and flush.