I think World Tournament IS canon because:
- it looks like Giovanni has sprite from HG/SS (third on the right on tournament table, I think it's him),
- look at battle titles for Cynthia, Steven, Lance and Gary. They all say "Pokemon Trainer" ポケモントレーナー there won't be problem if Giovanni is classified as still being Gym Leader because he's probably going to be simply called Pokemon Trainer,
- if it wasn't canon both Steven and Wallace would appear in Corocoro being labeled as Champions, but only Steven appeared. It also most likely indicates that B2/W2 take place before R/S/E.