Apparition, from its Latin base, simply means to appear, if suddenly. This can be seen in many definitions and dictionaries.
a supernatural appearance of a person orthing, especially a ghost; a specter orphantom; wraith. Dictionary.reference.com
ap·pa·ri·tion Origin late Middle English (in the sense ‘the action of appearing’): from Latin apparitio(n-) ‘attendance,’ from the verb apparere
The meaning of apparition in Harry Potter isn't really about the actual travel, but how they disappear and appear suddenly, as if into/out of nowhere.
While it hasn't been used in most media, the Harry Potter usage is in line with the basic definition, and could be called teleporting if Harry Potter was scifi, but since it's fantasy, it needs a spooky twist.