Super is a follow up to the two canon movies that Toriyama wrote due to not liking the current state of Dragon Ball and has written the outline for each arc of Super. There are various things that contradict EoZ/GT already, and there will only be more.Toriyama actually gave his approval to GT, and even designed some characters, and his son worked on the show as well. It's pretty official, way more so than Super, which Toriyama doesn't even contribute much to. He's watching these episodes just like we are, waiting to figure out what's coming next.
I have to say that if Super contradicts GT, then it'll basically be the definition of bad filler.