Yeah, but the anime DID throw any likeability of the characters away for me, which is immediately a drag down for everything else.

The way the girls interact with Keiichi all the way through the question arcs in the anime feel completely unnatural and creepy to me.

I don't know, i find them equally likable in anime and VN. There is simply one problem in anime - first two chapters are way too rushed and not that great overall(i mean, they are good, but not masterpiece level), so it takes some time for them to become actually compelling. I am referencing chapter 3 again hehe, but yeah, that's where i started to really like them.

Though, it was the case only when i was watching for the first time, right now i am rewatching anime(on season 2 already) and this time i just know who are they, so ofc i find them likable right from the start and understand their behavior in context of Keichi's paranoia which twists the reality and in context of additional stuff which i learned in VN which allows me to look at them deeper. So in my case reading VN didn't throw any likability from anime characters, but instead increased it, because i simply now know more about them!

Now, for the horror factor this is fine. But it puts a wrench in getting across why you should care that Keiichi's world is collapsing when it was all weird and fake feeling from the start.

Absolutely same thing - i remember what "Keichi's world" is. Maybe there isn't 5 hours long build up for that world, but that was a problem only for the first time. Right now, when i am rewatching, i already know what is collasping, so i just enjoy this side of the story.