Equestria Girls is canon in the same way the comics are. Canon or non-canon status is kept up to the viewer, unless the main show acknowledges or denies it. FiM is the most important and writers do not have to take the other two into account when making episodes.
All that pony Flash’s appearances confirm is that there’s a pony Flash, not that Equestria Girls ever happened. Same with Trixie liking peanut butter crackers… it just means she likes them, not that Equestria Girls ever happened. What we need is something that actually confirms it, like a glimpse of the mirror portal or a picture of Sunset Shimmer in either Twilight or Celestia’s room.
The most damning thing against EG being canon, to me, is that scene in Equestria Games where Twilight and Spike all but outright deny that the first movie happened. I doubt it was intentional, Dave Polsky probably didn’t even know EG’s plot, but it still stands.