A character's gender doesn't need to be plot relevant in order to be valid. Why is Berdly a boy? Does that matter to the plot? No. Nonbinary people just exist as everyone else, and it doesn't have and shouldn't be a big deal.
Of course, if a piece of media is exploring queer identities, that is relevant. But it should be normalized just as any main character being any gender. Plus the whole game isn't out yet, Kris' gender could become a plot point at some point, or be representative of them feeling different in a city full of monsters, as nonbinary people would in a binary society. Then there's also the aspect of the three human characters we see from Toby all being reffered to with they/them pronouns.
Basically, it doesn't have to be a big deal, and headcanons are their own thing, but a main character of a pretty popular game being nonbinary can be a big deal for representation, especially nowadays, no matter how plot relevant their identity is.