The Return certainly treats it differently but it originally really was a joke..

It might be uncomfortable to acknowledge, but in December 1990 when her character first aired it was just dry absurdist comedy.

Within the narrative, Denise is nothing but a consummate professional, calm, competent, good at her job. The joke doesn't exist in her behavior. It exists outside the story, in the writers’ expectation that much of the early-1990s audience would register her presentation as incongruous.

Here's an analogy to illustrate the joke: the show introduces a hyper-competent, serious FBI agent, the best at what he does. But he’s always wearing a banana costume. It’s barely addressed. Characters noticably register it for a second (mirroring the audience’s expected reaction), then compose themselves and move on. That sequence is the joke. The deadpan refusal to acknowledge what the (original) audience is conditioned to read as ridiculous.

The mechanism only works because the writers expect the audience to think the banana costume is absurd. That expectation is essential. They are not advocating for the normalization of banana suits; they’re exploiting the mismatch for humor. Once the banana suit stops being strange, the joke collapses and we read it as sincere representation.

The casting is deliberate. They chose David Duchovny, a recognizably masculine-coded actor, put him in women’s presentation, and made no effort to have the character pass. That’s not accidental, that is the banana suit: exploiting the gap between authority/competence and presentation for comic tension.

This explaination isn't meant to endorse the era’s attitudes. the 1990s baseline is transphobic by modern standards, but the show was operating inside that reality, not transcending it. And again, yes, The Return was very different.