Of course, patriarch theory completely accounts for this. The common view that men are more powerful and autonomous, and therefore dangerous, can probably account for some degree of their harsher treatment under the justice system, just like this view probably helps them in acquiring positions of power in the workplace.
I don't see how. If men are perceived as being stronger and more rational, that will help them in acquiring jobs, but hurt them when being found culpable of a crime.
I'm not sure where you learned feminist theory, but it's fairly resolute about the fact that Patriarchy is deleterious to both men and women.
Nobody learns feminist theory because it's not a learnable topic, it's just a collection of nonsensical anecdotes bound together with clever sounding words.
If men get sentenced more harshly because they are "stronger" and "more rational", or even just perceived that way, then there's no problem with them dominating roles that benefit from a lot of strength or rationality, roles like CEO of a company. But feminists have a big problem with that notion. They're all about how women are just as good as men at everything, equal in all respects and thus deserving of equal outcomes, right until there's an outcome that's better for women than men. Then suddenly there's an intellectual sounding but illogical explanation.
By the same standard, do you agree that there is systemic sexism against men?