Since the "malevolent phantom" refers to Boo Radley, the phrase is a metaphor as Scout makes an unstated comparison between Boo and the evil ghost/"malevolent phantom."  However, there is a bit of hyperbole attached to this metaphor since Boo Radley is hardly an evil ghost, and to call him "a malevolent phantom" is clearly an exaggeration. 

Of course in the final chapters, Scout learns that Boo Radley is truly a person and a person who possesses commendable characteristics, especially heroism.  But, in Chapter One, Scout and Jem believe that the Radley Place, which juts into a sharp curve beyond their house, is a strange and frightful place because the Radley's keep to themselves, and Boo has not been seen outside for years.  Superstitions are attached, then, to the Radley home.  None of the black community will walk past the house in the evening; supposedly people's chickens and household pets have been found mutilated; pecans shaken from the schoolyard tree that fell into the Radley yard were never touched.