Nope, using "gender" to describe a behaviour typical to (or typically used against) one sex is completely misleading in a world where "gender" is now used by most organisations etc to mean what you "identify" as.
A transwoman sexually assaulting a transman would fit a typical pattern of crimes based on their sex, but would be against normal patterns for their gender, for example.
Also, because "gender" is meant to be identifiable only by the individual (it's not meant to be judged from how they look, dress etc, only how they "identify"), that would mean we can only be sure it is "gender-based" violence if the perpetrator knew beforehand how the victim identified (if the attack was based purely on the person's visible sex, that proves it is NOT gender-based but sex-based surely, as the perp didn't care how they identify?), and if there is reason to believe that it would not have happened if they knew the victim identified differently to what they assumed. Do we have any evidence of people being asked how they identify before having violence perpetrated on them? In addition, it ought to imply that the same violence is also (or might be) committed against people of the other sex if they identified as that gender.
For example, has anyone ever avoided foot-binding or breast ironing by saying they feel like a boy actually, thanks very much? (On the contrary I read about at least one very sad case where a transman was raped by a man despite protesting repeatedly to the attacker that they were not a woman...). Similarly, has anyone EVER ironed the breasts or bound the feet of a transwoman?
If the answer to these questions is no, it's very clear that this is SEX-based violence, not gender (at least not in the current most-used sense of the term).