Happily! Because you know who’s trans?
This is mostly about her Fox-Men and X-Men: Evolution incarnations, because even though I love the franchise, I can’t keep up with the comics the way some people can, and I haven’t seen any of Wolverine and the X-men, so I can’t site anything from there.
This one may actually be cheating, because I don’t even think this is a headcannon. I’m 99% certain Rogue is a young-transitioning trans woman in-continuity. The whole “who I am naturally makes me untouchable and alone” motif is just… so… blatant.
In the old 90s animated series, her power set is specifically coded as masculine: super-strength, super-toughness, super-accent—and her core power of life-force-theft rarely comes up except for the drama value. She’s cursed with a past so mysterious, even she doesn’t know all of it, and we see a few episodes featuring Professor X helping her control and lock away negative aspects of her personality (these are painted up to look like the personality she took from Carol Danvers, but act nothing like Ms. Marvel and probably represent all kinds of buried self-loathing), analogues for trans women of the era being forced to hide their pasts by therapists of the day. And good lord do they sexualize her in that series.
In Evolution, they play up her “I’m untouchable” aspect rather than her being a sex-bomb, making a more honest and personal portrayal of being trans. She even has a more pronounced chin and wider shoulders than the other girls in the series. It’s revealed (spoiler warning) that Rogue is the daughter of Mystique, herself a shapeshifter to whom physical sex means squadoo, and was raised by a mutant with the power to see the future and know that 1) little baby Rogue would grow up into a woman, and 2) little baby Rogue would never be happy as a boy.
So little Rogue is born to her shapeshifting, on-the-go mommy (or possibly daddy), and handed off to a guardian who already knows she grows up to be a healthy girl. Mystique doesn’t care either way, and so from a young age Rogue gets to be a happy, healthy little girl. Until her powers erupt as a metaphor for the more traditional trans girl experience.