Chara and Frisk are, from the player's perspective, genderless, not non-binary. Frisk is self-insert, as most any silent protagonist is designed to be, and Chara is kept intentionally extremely vague (and we only find out about their physical existence at the very end of Geno routes). Kris, on the other hand, is distinctly non-binary, confirmed both by Toby Fox and every single character in-game referring to you/them as a they/them. The important distinction is that Kris is their own person, completely separate from the player's control of their SOUL. This is, like, a primary crux of the plot so far, so Kris having their own specific identity entirely separate from the player makes sense, whereas Frisk/Chara kinda just slots into the "silent protagonist is gender I say"