One thing to realize is that, when you are seeing bodybuilders on stage with 3 percent body fat, everything is geared towards showing off that low body fat. They are completely shaved, oiled up, bronzed, with appropriate stage lighting, water depleted, carb depleted, and flexing to the max. And many other tricks body builders do.
Cavill was doing none of these things, he was extremely pale, very hairy, in very flat drab lighting (actually horrible lighting) and not flexing at all. It is entirely different circumstances. He was just playing a normal man stealing some clothes and running away. I daresay you would see much more of his muscle definition if he did a body building photo shoot with all the bells and whistles.
But this much is certain he had low body fat. Look at the pictures below.
Abs are bulging but look at the arms. Look at the separation between the biceps and the delts, and the pecs and the delts, he is very sharply cut. This kind of sharp appearance comes with low body fat. So even though he might not be 3%, he's definitely single digit.
And both Twight, Snyder and Cavill claimed that figure so it wouldn't be very far off the mark. Cavill very widely claimed that he was at 6% body fat in Immortals. And he looks much much sharply defined in MOS. So he might be around that number.
But remember, the physiques of body builders and actors are presented in extremely different circumstances. It is actually a very disadvantageous way for the actors to present their results, because they just do an incidental scene in films.