If she does (claim she) regards them that way, it’s not obvious from the article.
If she is claiming that, surely she ought to be stating very clearly that the starting point should be that all such “women” should be in the women’s estate automatically and should only be placed in the male estate if they are exceptionally violent or are risk assessed as presenting such a risk to the other prisoners in the women’s estate as to justify it. In theory, women can be placed in the male estate, though I understand it never happens. If she thinks these men should be treated as if they were women, that ought to be what occurs.
In the sentences I quoted, she compares “trans women” with “cis men”, surely implying she regards both as male? I note she’s very cagey throughout, referring to “trans prisoners” regularly rather than acknowledging which subset present specific risks.
So I expect you are correct, because literally the only logical reason that men who claim they are women should be placed in the women’s estate would be if you believed them actually to be women (hence all the mantras, trying to embed that idea by repetition), but that she is unable to make that argument with any clarity either means that she can’t bring herself to say it because she knows nobody actually believes it, or (and this is possible from the other comments above) she is simply such a poor writer that she is unable to make one, single clear point about the argument she is trying to make.
It’s probably the latter, isn’t it? 🤣