This is the same energy that Redditors make where they claim Piccolo from Dragon Ball is "Black Coded".
So let's look at two obvious reasons why Samus is not some propaganda piece for troons.
1. Nintendo explicitly wanted Metroid for the NES/Famicom to have a twist ending just like in the 1979 horror movie 'Alien'. Anyone that saw Alien for the first time probably remember how they didn't expect the character Ellen Ripley to be the real hero of the movie where she survives and leaves that xenomorth for dead in the vacuum of space as she is the only survivor of her crew and she flies back home. It's the same with Samus where first time players of Metroid back in the day didn't knew that Samus was a woman until they beat the game. This was just Nintendo's own take on the concept that the movie Alien used to make the game more memorable.
2. The OG Metreoid games were made at a time long before LGBT-related anything became mainstream. Back in the day, shit like LGBT content was still a niche form of media, when the LGBT rights movement was still in its infancy, and when DEI/ESG initiatives didn't existed. Even back in the 1980's and the 1990's, everybody knew what a homosexual is (although in a negative light due to how social attitudes towards homosexuality was like back then) but things like transgenderisim wouldn't enter the mainstream public lexicon until the 2000's when the LGBT rights movement really started to kick into high gear. Most people back in the 80's and 90's didn't even knew what is a transgender person, so the idea that Samus was meant to troon people out is fucking laughable.
It's really laughably retarded to apply modern standards to things of the past, especially when you were never around to experience the past or when you don't understand the context of what things were like at the time to make a fair judgement.