I understand where you are coming from with this, but I have to disagree with some of it. First, let me tell of my background. I didn't transition nearly as long ago as you did, but I have been on Estradiol over 9 years, lived as myself for almost 9 years, and had bottom surgery over 3 years ago. I waited many years to transition because of internalized transphobia mixed with denial.
I identified as a cross dresser for many years before I finally admitted to myself that I was trans. New information at the time (like that cross dressing wasn't a "paraphilia," that autogynaphilia was a debunked theory) helped me understand that I am really a trans woman.
I don't know which, if any, of my experiences you can identify with, but I don't think you have to do so in order to see the points I want to make.
So please excuse the longwinded prelude and I will state my points:
First and foremost, it seems to go beyond fear for Rowling.
If it were a matter of the kind of fear you were talking about, she might say she is suspicious of early transitioners and trans feminine non-binary people in women's spaces (which can be problematic in itself). However, she is not just saying she doesn't trust someone who "looks trans" (whatever that means), but she is excluding you, me, any other trans women whether we have medically transitioned, whether we "pass" (whatever that means) or not. If I am reading her correctly (and I pray I am not, but don't hold out much hope), she is saying that trans women, just by virtue of having been assigned male at birth, do not have the right to the same spaces as cisgender women. In other words, you and I don't belong in women's bathrooms, changing rooms, etc. because we were assigned male at birth. Although she can't possibly know the circumstances of most other people's birth, she seems to place undue emphasis on it. If it were really about this very real fear you have hit on, the circumstances of our birth shouldn't matter.
I understand fear, especially by women of men, but don't buy the idea that that fear excuses or even explains singling out of trans women, especially when the argument made by Rowling and others relies on sex. Trans men are mostly assigned female at birth and often still have the genitals they were born with. Basing the separation on just sex, as Rowling and others seem to endorse, would mean trans men could walk into a women's bathroom without impunity. I would be much more fearful in that situation than if a recognizably trans feminine person walked in. I think most women would.
My point is that, although the fear you mention is valid and common, the idea that it should be aimed mostly at trans women (and make no mistake: it is) is not. Simply put, discriminating against women and feminine NB people because of fear of men not only makes no sense, it is bigotry.
I would also challenge your assertion that people who have not lived as women for a long time like you or I have cannot understand the "very real threat" that we live with. I remember my life pre-transition. Whenever I left the house dressed in women's clothing, in makeup, etc., I feared for my life. Just because I still was technically male, and would change out of those clothes and wash off the makeup (reluctantly) when I got home didn't mean that made any difference to men with ill intent. In fact, it had the opposite effect. Men either felt entitled to me sexually because I was dressed as a woman (especially at parties and clubs, dressed somewhat sexily), or sought to hurt me to police my gender. In other words, almost all trans-feminine people know that same fear. And, not to put a fine on it, but they, too, need a place to pee. They have the same rights to not be molested, to be as free from fear as possible, as anyone else.
So I understand and even share Rowling's fear. But it doesn't follow that that fear should be of trans people. True, it is easy to feel powerless as a woman in this world; sometimes nowhere feels safe. Hell, sometimes no where is safe. But that's just it: regulating your fellow inhabitants of the bathroom just to those who look just like you won't keep you safe. Furthermore, I believe most cis women know this and are perfectly capable of making the very clear distinction between a trans woman (even early in transition) and a man.
I deeply appreciate your comments and the opportunity to present my perspective. I will read the story you linked in your comment.