It's not even a modern trans issue. It's basic respect for creators and that's what I find annoying about trying to declare it a certainty or canon or whatever they'd like to call it.
At the end of the day, it is most typical and expected that a character's creator and not a character's fans define said character. Not in every last case, but yeah, most of the time.
With something like this, a mass media character who's been touched by many hands, the waters are of course a bit muddier, but it's not an impossible problem by any means. In Metroid's case, it's generally accepted that, Samus' concept is credited to Makoto Kano while credit for the design is given to Hiroji Kiyotake. In addition, there's a documented history that she was largely based on Ellen Ripley (among other characters) and the staff held a vote to decide the character was simply female - one presumes that no mention of dickgirls was made at the meeting (or at least I feel it's fair to assume this unless other Nintendo staffers step forward to state that that was actually the case).
By the same token, other big franchises may have many staff who create stories for a character, but when there's confusion the typical answer is to go back to the original creator. Thousands of people have told official stories about Luke Skywalker, but if there's ever a conflict it is generally agreed that George Lucas would have final say. Even with the sale of the property and the loss of Lucas' legal standing, Disney's credibility as the owner in some ways rests on not directly contradicting this, at least not explicitly while Lucas is alive.
So how about Hirofumi? Does he have any standing to impose his view, joke or not? Well as it turns out he wasn't a one of Samus primary creators. Nor was he team lead. Nor did he ever work directly on Samus concept, design, or implementation in any capacity. What he was was one of several background graphics designers; in essence a relatively minor member of a fair-sized staff. So my bet is prrrroobably not.
The flip side of this is that when a creator says something about their own character outside the original publication, we generally accept it. Albus Dumbledore is one of the best recent examples. We accept him as a gay character because even though Rowling did not explicitly write this in the book, she has stated that this is the case. You can't choose to defer to the creator when it suits you but override them when it doesn't. Well, you can, but it's cognitively dissonant.
I mean, I'm basically with Grath. These things become arguments because people are rightly upset they have no representation. The answer to that is not to force square pegs into round holes. The answer is real representation.