Is "Phantom Rouge" story canon? Simply that: did the events of Hunter x Hunter: Phantom Rouge really happen (with respect to HxH story, of course)? At least the timeline is credible (between Yorknew City and Greed Island arcs).
It's a part-canon side-story.

AniDB:


  The premise of the movie is based off a manuscript of the Yorknew City arc written by Togashi Yoshihiro that he eventually ended up scrapping.


WP:


  The film is based on an unpublished story manga creator Yoshihiro Togashi wrote around 10 years ago.


Since it's based off his own work, Phantom Rouge presumably has Togashi's blessings.