Reading that string of tweets, it doesn't seem like the writings of an outright transphobe as much as the writings of someone who doesn't have a way with words. Which is odd, for a writer, but considering the subject matter more than understandable. Half of the words she used have been ascribed multiple meanings by now, and it's easy to get tangled up in your own web of arguments.
As for the new book, I haven't read it, but it sounds more like an attack on transvestites than trans people. It's not like evil cross dressers don't exist, but a story like that usually benefits from showing another cross dresser that isn't evil just to reassure the audience that crossdressing=evil is not the message they should take away from it.
I'm guessing that's just a big fail on her part, rather than malicious intent.
As for her other posts on twitter, most of what I'm seeing is poor word choice, genuine confusion and genuine concern. Is it misguided? Perhaps, i won't be the judge of that. But she's no villain for questioning these things. If it weren't for questioning things, the lgbt community wouldn't be as prosperous as it is today. Adverse arguments provide opportunity for refinement.