There were several hints in the game that Varik was supposed to be (a future?) Ness. The game calls you "Giygas slayer" at times, and people mistake you for Ness a lot. Radiation said that it just started with him "wanting to look lazy" by not editing Ness's death sprite, but then decided to keep going, since Ness and Varik are both blank, mute heroes. He said it's up to you to decide if they really are the same person.
There was also hints that Varik's intrusion upon Dr. Andonuts' Magicant was corrupting it, since there were places and people only Varik/Ness would remember. Radiation also said this just sort of happened.