But stats (at least here in the U.S) already take into account an estimation of unreported rapes though, and female perpetrators are less likely to be reported, that is true. But researchers are aware of that and factor that in when doing the statistical analysis. In the U.S it's 99%.
The bias you are talking about is not structural at all. That means that the bias is built into the system specifically to advantage women, and that is clearly not true. Society was built by men and only for men originally. The bias in the criminal justice systems comes from exactly what I already said. The relatively high amount of male perpetrators compared to women along with the fact that male perpetrators are more likely to be repeat offenders and to be more brutal and cause more severe injuries. That is what creates bias in male judges. That and the stigma against male victims that again, comes from women being unequal. The structural issues negatively effect men, but they come from women's disadvantages and inquality, not mens. There IS a violence issue among men, that's not just baseless sexism