It's canon in the sense that it had happened in lore but in another timeline. The way I choose to think of it is based on popular opinion is that GT is a continuation of the movie timeline.The movies seem to follow the regular timeline but veer off at certain points to add more. GT can then have it's "Super" moment of meeting the higher stakes of Gods and stuff but just later than the Super timeline. Simple enough to not ruin the character development in either timeline and hold true to each fanbase.