In a nutshell: droop has two sources - first mechanical alignment of the barrel with the receiver and second optical alignment of the scope's visual axis with the bore. This is likely the most important source of droop.
A pellet's trajectory will ensure that it will initially be below the line of sight (i.e. the point of aim); then it will be above the POA; then it will fall below it again, never to cross the line of sight again.