Most crimes like this will be reported as "man suspected of X," and it is assumed by default that the man in question is cisgender so, there's no apparent need to make that distinction (there should be, but there isn't). In this case, I think it's actually appropriate for them to report his gender identity because it brings up the very real facts that 1) female-bodied people, including transgender men, are equally capable of (sexual) violence as those who are male-bodied, and 2) trans-on-trans violence does exist and should not be assumed not to, or lumped in a category of "what those people do to each other doesn't matter." It matters. If this story turns out to be true, it's a case of a grown man sexually abusing a child, and he should be punished accordingly - by being sent to prison with other men who molest children, and let the general population see what they think of him just like anyone else.
If this is true, not only did this man commit just about the worst crime possible, he may also have permanently ruined this child's mental health (and any chances of medically transitioning if they want). My hope here is that this case is taken as seriously as it should be, and that sexism doesn't come into play to absolve him of his crimes by virtue of having been born female - now, if knowing that he's transgender does bias the court in that way, I will agree that they should not have reported nor disclosed to the court his gender identity because it does not matter, and he absolutely should not be offered any special protections because of it.
