I think it is fair enough that if someone beats up a bloke for 'looking gay' it should be a hate crime. Just as burning down a shop and writing "burn in hell [insert racial slur]" should be treated as hate, because it is the intent of the perpetrator is what is the issue. They are the sort of person that hate people of a particular group so much they would commit arson or battery to vent that hate.
My fear in all this is that women with penises will exploit this law for validation and waste lots of police time, whereas women and girls will continue to suck all the abuse back up as normal, because of our conditioning.
Also, I think "women" like Paris Lees actually like sexual harassment and would find being called a 'dirty slag' as they go about their business wonderfully validating, so it wouldn't surprise me if such people would be very much opposed to making misogyny a hate crime.
I can just imagine the scenario where a "woman" puts in a complaint of misogyny, and the perpetrator says "no I hate them because of the gender reassignment and homophobia, not because I believe they are a woman guv".