I think there are three things here.
One is that trans people will face disadvantage, harm and abuse because their gender expression varies from the norm. I think any attempt to deny that flies against common sense. We live in a misogynist world, and violent men police gender conformity as part of that.
Two is that false stats are thrown about so commonly (the murder rate being the obvious one, though there are several more examples) and some stats are so unreliable (a self-determined record of what counts as a hate incident, even where it could arguably count as one against women) that people are instinctively sceptical.
Thirdly is that the majority of violent crime affects men - both as perpetrator, and as victim (the exception being sexual crime, where most victims are women). It is not women's responsibility to give up our own protections, provisions and rights to protect one group of male people from another. We are not human shields for male violence and abuse.
All three statements are true.