I'm not familiar with Terry Pratchett, but I'd give a very high chance of him supporting trans stuff and continuing to support it in the Current Year, simply by virtue of him being a fantasy author.
Most of whom would at least
claim to support trans people. And they probably all believe that they do. They're almost all progressives. And to them, supporting trans just means supporting people to be their true and authentic selves. If they have any nagging doubts about the sinister side of transness, like the coercion of children, then they either keep these things to themselves, or they think these things are so rare that they're not even worth talking about.
(Being in a progressive echo chamber will do that to you, when every "authoritative" source of information paints trans in such a positive light, and any opposition to trans ideology comes from "far-right" people they wouldn't want to talk to anyway.)
Remember that noted transphobe J. K. Rowling
also supports trans people. She even said in the essay that got her cancelled that trans women are in some ways
more oppressed than women. If anything, her cancellation was for not going far enough, for drawing a line in sand and saying she would only support them
up to a point.
And while Pratchett may not have written about guys chopping their dicks off, he also wouldn't have needed to. You can just write about someone
wanting to be a different gender, and half the people who desire trans representation will see it in this character (the other half will insist that the character isn't trans enough, and needs to be transed up further). And since it's fantasy, you can always use some kind of magical plot device to change someone's sex (which is pretty much how trans people view HRT).
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A quick scan of TVTropes would imply (correct me if I'm wrong) he believed the differences between genders are largely social. People who think this are very easily conned into thinking their beliefs equate to gender being
entirely social. Of course, it's possible the example mentioned about Eskarina's magic is merely symbolic of a woman breaking the proverbial glass ceiling, But even if he'd lived to 2021, I doubt Pratchett would be such a sperg that he'd go out his way to say you
can't interpret it also as a metaphor for being trans.