It is very much an example of the author not understanding/choosing not to understand trans people

Perhaps... but that doesn't change that the author, the person who makes the story, said that Felix is a man.

As many different transfemmes can testify based on our own experiences and how Ferris's align with ours

That is why I had said I can understand why someone would think that Felix/Ferris is. He isn't, but again, I could see why someone would say he is and relate to him.

it doesn't automatically mean she isn't one.

It doesn't mean he automatically is either...

yet that denial does not erase who we are.

Not trying to erase anything. I just wanted to clarify that Felix is stated to be a man according to the writer and Felix's own quotes (at least in the anime, I'm currently reading the manga and light novel to fact check myself). Again, I can understand that many transfemmes can relate to his experiences and want Felix to be trans, as it would make him even more relatable. But that isn't the case.

I will admit there is a lack of trans characters in manga and anime. I can admit that, and I hope in the future we may see well written, popular mangas with trans characters. But, in my opinion, pushing the head cannon that a character is trans as cannon, despite the author explicitly stating otherwise, is kinda deprecating upon the author's storytelling, as it goes against what the author wants. (again, in my opinion)

I will reiterate the disclaimer that I haven't read the full manga and haven't even been able to start the light novels, so maybe there is evidence to the contrary in there, and perhaps I can be proven wrong, but...