The notion that Equestria Girls isn't canon remains a very legitimate position. FiM has gone almost out of its way to deny that any Equestria Girls film has happened.
Case in point, the portal. It's now in Twilight's castle, presumably in her library, and yet not once did we see it throughout season 5, despite seeing her library multiple times. Something like that would have been "be all, end all" confirmation of its canonicity. And yet, it wasn't there, nor was there even the slightest reference to the films to be found in all of season 5.
The films can make all the references to the show that they want, but at the end of the day, all that proves is that FiM is canon to Equestria Girls (which should be obvious anyway). It DOES NOT prove the opposite.
So yes, as far as I'm concerned, Equestria Girls is non-canon to FiM and it will remain that way until I see evidence to the contrary.