I guess it depends whether you accept that Agatha Trunchbull is a TIM. It would seem so that she's an olympic hammer thrower and women weren't allowed to compete in the olympics according to the article so would suggest maybe she's trans. I don't read the story that way, to me she's a woman albeit not a stereotypical one and i think the character is stronger for that.
I would have said there's a sexist element to it, except that matilda's mother who is traditionally feminine and "chooses looks" is also a horrible person. As is her father, who is vain and crooked. I think the message isn't that trunchbull is hated because of her masculine appearance. Shes hated because she's a bully who uses her physical strength to terrorise children. Miss honey is a hero because she's kind, treats other people well and with consideration, is clever and appreciates the value of knowledge. Her character would work just as well if she were ugly.
I think as the author is only looking at the stage shows they will see men playing the role and assume that its transphobic. But isn't it sexist to assume a large masculine woman is really a man? isn't it sexist to cast a man in a female role? Pam ferris was probably the most perfectly cast actor in the film version and she's a woman. Personally I don't think female roles should be played by men, just as white actors shouldn't play parts that are written for black actors. The stage show turned the trunchbull into a pantomime dame and you didn't get any sense of menace because she was a figure of ridicule. It changed the slant of the story and not for the better in my view.