But that's one scene, and there's no need to show his crotch during that scene. After the transformation, he gets some pants.
Johnny would also burn his clothes off, but he wouldn't just walk around naked after that (and I suspect they'll find some way to avoid showing MBJ's crotch on screen after he has burned his clothes off).
And it's not just that it looks ridiculous and will lead to giggles and jokes during the film - it's counter to the character.
We all know that, beneath his tough surface, Ben is actually sort of sensitive, shy and wants more than anything to fit in. He wouldn't just say: "Oh, look, I've got no d***. Hey world! Look at me, I've got no d***!"
He'd be embarrassed and he'd put some pants on.