The ARG shit I understand, even if I dislike it. It drives engagement and terminally online autists who datamine games love that shit, but it does mean the game is no longer a packaged and done deal, which may be fine for a story-first 'game' like Deltarune, but is out-of-place in pretty much everything else. And that's the point, it's not a game first, it's an interactive story first. Of course the RPG part is bad when it's in the sole service of a narrative. The "they" part is part of the narrative too: I believe that it's not a "they" as in "I don't know what gender they are because they are wearing a mask and not talking" but a "they" as in "they are two people/entities", so it cannot be solved by "picking he/her", as that would only confuse things further and maybe even give ammo to the genderspecials. But I nor nobody else can know for sure because the story ain't finished, and it sure is weird that everyone is referring to a boy as "they". Coupled with the ARGs and whatnot, the game might be huffing its own farts a bit much, and there's reason to doubt that all the various plot hooks actually catch on by the end, but it's still a cohesive narrative that is, unfortunately, built around many people crawling over every surface and resource the game has, similarly to how Undertale had to be decompiled to get at any of the "Gaster" shit.
I respect your ability to pick negatives in a thing you still clearly like; That being said, I will sperg onward:
The ARG, I believe, is just filler for attention - as you have also said it drives engagement. But, in my opinion it's still a negative, since this means the game itself is not engaging enough without the ARG element. ARG's have been in games for some time now, but almost every time they're introduced is when the engagement with the product is waning.
About Kris - this is an issue Toby has created himself. Clearly, he's not skilled enough in writing to handle both a story where the controller character is their own entity, and this meta aspect about the 4th wall being broken; So now he has to balance the character as an IN GAME character, and as a tool to realise his hypothetical about player characters being unwilling participants in the plans of the person behind the screen. The issues stems from the game lacking immersion, just like Undertale did - One cannot just let themselves imagine that they have taken the role of a character within the world, they are constantly bombarded with reminders that - "YOU'RE IN A GAME! DID YOU NOW THAT YOU'RE IN A GAME?!!!?!?!? YOU'RE THE PLAYER CONTROLLING A CHARACTER!!!!". It would be more impactful if the 4th wall breaks were subtle, at least.
Just like when you read a book, it's obvious that you're reading words on paper - but if the writing is good, it makes it all compelling enough for you to vividly imagine the described events. That's why I said that a simple character customisation mechanic would fair better - Toby isn't skilled enough to do otherwise. And that's why both Undertale and Deltarune are considered pretencious by it's critics (And me, obviously). It doesn't matter if it was intended to be an "interactive story" or not, it's not executed well enough for that to be understood right away. And "interactive stories" usually limit player's decision making ability, to hammer the point in.
One more point is that the story is overly-reliant on being depicted within a video game. A good story should be able to stand on it's own when, for example, just written out for someone to read. I'll provide an example - the METRO games were based on a book series of the same name by russian author Dmitry Glukhovsky; After the success of multiple game titles, Glukhovsky took the last released game in the series as a basis for his next book - which meant that both the video game, and both the written variant of the story were executed so well that they became symbiotic. Deltarune and Undertale could never do that, because they were created explicitly to be meta-games, they're too detached from reality to be relatable in story form (And all good literature has some kind of reference to real events, to set up a framework, even if it's fantasy or sci-fi). So much explanations and autistic trivia would be needed to depict Deltarune purely in text form, with author's intentions in mind, it'd be some discount-bin level fiction.
That xitter screenshot only adds to my dislike of Toby and his games - I can't take this guy seriously; He already got clout from his amateurish creations, and is still insecure in the decisions he makes - at least be bold, even if you're working for an audience with low standards. Also just blatantly admitting that you constantly regurgitate one idea over and over again.
TL;DR: Tobias Fox overestimates his writing skills, which causes problems in self-expression.