Well I have now sussed out that the 100% game completion includes the challenge mode, not just the story.
As far as the ingame medals go for the challenges (not the trophies), I have managed to get all 3 medals for all the predator challenges, expect one, as its almost impossible to get the two that I have been trying to get.
As for the fighting challenges, I dont see me ever getting all three medals on some of them.

These challenges are really for true hardcore gamers, who take this shit seriously.

The Joker challenges are fucking hard as well, because you dont have the gadgets available to you like you do with Bats.
All you get is a pair of x-ray specs, which unlike the detective vision, cannot be left on.
You also get a pair of Joker teeth and a gun, but both are only good for one shot.
You can grapple, cant glide and have no way of doing most of what Batman can do.