What complicates this, is that we're talking about fictional characters. For those, everything gets filtered through the lens of the author, reflecting all of their biases and prejudices. We're going off second-hand information, basically. In such a situation, coding becomes much more vital when analyzing characters, I think. A character being referred to and referring to themselves as masculine might be because they are, or it might reflect the author's perception of trans people. It'd be easier in a work that already includes queer characters, because then the author would've already demonstrated understanding for their identities, and it would be easier to take them at their word.

In the case of Ferris, we have a character that presents feminine, displays emotions and struggles trans people are all too familiar with, and in the narrative it's stated that she should've been a woman. But she's consistently refered to by masculine pronouns.

There's nothing wrong with simply reading her character as cis (even though most people that are adamant on that point have very icky opinions on real trans people). As a work of art, that interpretation is up to the reader. But, imo, doing so glosses over many queer themes, in a medium that is already starved for representation.

Another example that often gets brought up in discussions like this is Lukako from Steins;Gate. She also gets referred to by masculine pronouns throughout most of it. But then there is an arc where she begs the MC to use time travel shenanigans to turn her into a girl. This works, and she is noticeably happier in that world line. Then plot happens, and they have to revert the worldline, undoing that change. After that, the MC goes right back to calling her by masculine pronouns.

Once again, I would argue that her character is obviously written as trans, but in a medium and for an audience that are, for a large part, either ignorant of or hostile towards trans people.

This got way longer than I intended, sorry for the wall of text ^-^ One could probably make a two hour video essay on the topic and still miss nuances, and there's more I want to say, but this is long enough already. I hope I made my position a bit more clear, though c: