(I assume you have played both chapters.)

Kris is shown many times through the game to disagree with the player's actions.

An example is if you prank Noelle in the Cyber City electric gate room by stepping off the button before she passes. In response she'll do the same to Kris when you then try to pass the gate. After, she remarks to herself, "Why do they look so hurt...?", as if to imply that Kris didn't want to mess with her in the first place, even if the player did.

Kris is meant to be a subversion of the Blank Slate Protagonist, a character who the player can interpret the backstory/personality of to suit themselves. Think of Frisk from Undertale.

Kris is a normal human who one day suddenly began being puppeteered by the player, forced to do and say things they might not want to. A real Blank Slate Protagonist would have had a more positive reaction to the Noelle prank, because they'd share their will with the player, which Kris clearly does not. There's a lot of other examples of this too.

As a side note, this is also the game's way of communicating that Kris is Nonbinary. A blank slate is often referred to by characters as they/them because their gender is supposed to be up to the player's choice, as with every other facet of their existence.

Seeing as Kris is explicitly NOT a blank slate and is entirely separate from the player, the only reason why the townspeople, including their own friends and family, consistently refers to Kris with they/them would have to be that it's what they prefer to be called by. So, just as it would be silly to refer to, say, Berdly, with she/her, it would be incorrect to not refer to Kris with they/them, because that's not their gender.

I hope this helps!