Toriyama wasn't involved with GT that's why it was non canon. If he's involved that means it's gonna be canon. and apparently he's doing ss4 his way not GT's way and adding ss5 for real
well the series he was involved with were canon, and at least the Bardok movie was. But yeah forgot about the movies, so mostly his involvement means canon unless he says otherwise.
Does that mean that if its true on the SS5 thing that Goku vs Thor would take a level-up in intrigue again? YIKES!!!! Now if only Arc System Works could get some of the crew together to carry on with the main Guilty Gear storylines already.
Cross, until the show is on, it is pointless to guess how it will affect the series, Goku could get a major power boost, or not. We don't know what any of this is going to look like.
Even then he doesn't really have the destructive capacity to stop Thor, Mjolir block's galaxy to 1/5th of the universe busting attacks, unless Goku is turned into a universe buster (and since it actually turns out it's a inbetween chapters of Buu saga movie)then he would likely still fail. Plus he prefers melee normally, and I don't think he can do much to Thor