It seems to me the main reason a huge number of brony's are so set on labeling Equestria Girls as 'non cannon' is mainly due to the fact that if it were to be declared 'cannon' it would mean that the following themes will have been legitimized.
1. A magical gateway between Equestria and Earth
2. Humanized ponies
3. Ponies falling for humans
So given the fandom's ongoing love/hate relationship with these themes, I'm not the least bit surprised that so many have declared this movies as something that exists outside of the established universe.
Folks, the simple fact is that Twilight WAS attracted to Flash. Perhaps the reasons were a bit flimsy but the genuine attraction was there and it had nothing to do with Twilight's system being confused by her human body. She knew she was a pony, she thought like a pony, moved like a pony and even ate like a pony (at least until an odd look from Fluttershy broke her of that).
So despite the fact that Twilight was in the 'guise' of a human, her mind was still very much equine in nature. I use the moment when Flash asks her to be his date for the dance as my primary example. When asked, Twilight responds by pressing herself close to him in very pony-like manner.