I think it was actually some bullshit trend started by our dear John "Brianna Wu" Flynt, basing his claims on something one dev of the original Metroid said. It wasn't the creator, a lead dev, or a character designer, or a writer, or anything important; if I recall correctly, he did I think some part of map design or something like that, and said that he thought of Samus as a man initially or something like that.
Johnny boy ran with it as UNDENIABLE PROOF that Samus is trans, and the trannies took it as gospel, despite mountains of evidence, from all the info about Samus from subsequent games (the first one didn't have much info, as you may know it only reveals Samus is a woman at the very end, and does so only visually), or even the official manga commissioned by Nintendo, that clearly shows a young Samus as a little girl.
BUT NO, SAMUS IS TRANS BECAUSE SOME GUY WHO DID GRAPHIC TILESETS OR SOME SHIT SAID SOMETHING THAT COULD BE INTERPRETED THAT WAY IF YOU SQUINT, AND IF IT EVEN WAS TRANSLATED ACCURATELY TO BEGIN WITH