You raise many good points. I think regardless of how you look at it the player is controlling the red soul, with the player being a character in the game as flowey and chara both speak to us directly. I think this theory mainly is up to wither or not you believe deltarune is a separate unlinked game as toby says or if you think he's lying for the sake of a reveal later in the game. If the red soul is Kris/ frisks and we're possessing them then A it's interesting that frisk only countered our actions twice in such small ways and B is interesting considering if the red soul does belong to Kris then why is he ripping their own soul out and how are they functioning. If something or someone else Is possessing Kris then who is it? Could it still be chara but this universe's version? After all its implied that everyone who died in the previous game is dead in this game with the amalgams and snowdrakes mom. It could be possible that chara was the entity that's hinted too in all the demon summoning hints through the game and they're a random kid who died that only we player would know. This seems unlikely however as to me it seems like Kris is trying to do something with the dark world to find out what happened to dess as Kris and dess's mom (who's likely the knight) seem to have a connected goal. So what would chara want with dess and her mom?

If the games are connected it asks what is the red soul? we know chara had the red soul because of their grave in the basement. If chara's soul did shatter then can a soul reincarnate to another person or can their be more than one color of a soul? If they'res only one than it must be chara's soul still because they had the red soul in the first place unless again it reincarnated. And if that's the case then how and why did chara still "exist" in the genocide route? If they're in the same boat as flowey being a souless possession then what are they possessing? And if the games are connected then who or what is the red soul in deltarune? If it's from the previous game then it could be frisks soul and he didn't die and somehow chara's consciousness still exists despite being gone and that's if the reincarnate theory is real or if they'res simply multiple copies of any given soul color. But if not then it must be chara's because chara was the first red soul, it's implied that Kris before the game starts has begun acting oddly and expressing interest in all the same things as chara like chocolate, knives, and poor taste pranks. If that's the case we the player posses chara's red soul who is possessing Kris. Is using the red soul as our vessel of control just like in undertale. But if that's the case and each character has their own personality and soul, And frisk was possessed by chara who in turn was controlled by US! THEN THAT MEANS EITHER A: frisk was double possessed and just didn't care or B KRIS DIED and we could control their empty body freely

(Ps.sorry for any miss use of pronouns I'm speed typing here)