I'm almost certain they DO expect you to take it that way. The English localizers kept trying to make Marina seem less gay in Splatoon 2 so they let her fuck in 3 to atone
Nintendo Are Fascists answer: trans people are great to assimilate if they're straight
Nintendo is a corporation answer: they probably just didn't control their image quite as tightly back then, they let Golgo 13 onto the NES, and made Captain Rainbow which has bathroom transphobia innit
It's a Japanese culture thing, not a Nintendo thing.
Japan - and a lot of other countries, Iran being a big example - take the Transmedicalist view as mainstream. They value cultural assimilation along gender lines, but also understand that a trans person is not their AGAB. So as long as you do everything in your power to comform to your preferred gender, most (but not all) people will accept you. Being trans is fine; being "queer" is not.
They're not ALL kids haha. These two are in their 20s... otherwise Marina would probably get to wear a shirt over her bra.
Come to think of it, the protagonist is at least 19 now due to how time works. I think this is the first time you play as an adult! Not that the design aged any.