Wait, are you saying education system in general is broken? Absolutely agreed. It's just not the topic in question.
In a better system there would be no grades, but as long as we have a system centered around grades and discussing an article about gender bias in grading that's the topic. And within it it's bordering on deliberate, malevolent ignorance to say "oh no, boys are being mistreated by receiving slightly worse grades" without acknowledging that before that girls were discriminated against incomparably more strongly and while it's not ideal it would seem as if there are attempts to improve the system here.
The original argument was that there was an unconscious bias against girls before, and I posit that conscious bias is the only way to correct for unconscious bias, and sometimes conscious bias overcompensates without any ill intent (because humans are complicated and your unconscious bias against a person is not something you can measure with a stick, my wild guess is the "unconscious" part might have something to do with that). Someone tell me this is wrong, I am yet to see a single argument how.
Second, one of the guesses in the conclusions section of the paper explicitly states that it could all be simply the effect of teachers trying to use whatever they think is effective for the betterment of the students: they might think boys would be motivated to work harder if they are given lower grades while to girls failure is destructive and they need constant encouragement. Is the original intent good? Sure why not. Is this sexist though? Absolutely. Is withholding failure from girls only strengthens fear of failure in them, hurting them in the long run, while making boys more prepared for competitive environment outside the school system? Should this be more of concern than hurting boys by giving them slightly lower grades? I'd say so.