Probably because there's no "sexually explicit conduct" involved.
I have not seen the movie so I really have no standing.
From what I have read about the movie, here and in other places, the rape scene is pretty realistic but does not include film shots of actual penetration.
So you may be right, it does not actually depict actual rape. But the second snippet of US Code I posted mentions "or appears to show" explicit acts.
This was put in because of cases where the kids acted out scenes, without "doing it", to avoid prosecution as pornography under 2251.
I guess these guys found a loophole, or are willing to go to court to prove they have one.