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It’s the b-plot from what I recall, it’s not the main focus of the episode.
It was written long before his TERF days and so it’s not exactly hateful, just ignorant and it’s comparable to a lot of other ways comedy treated trans characters from the era - The League Of Gentleman was much, much worse than the IT Crowd imo, and that was a recurring character in every episode.
It’s rather the issue that while Matt Berry has distanced himself from the episode Linehan actually still defends it as pro-trans.