I admit that I don't like the UnderTale reference, but otherwise I am impressed. I like the idea of a living weather system; and from a gameplay perspective it makes sense that at least some of them, if we could ever be so lucky, would be triggered by events in-game.
Ironically, even though I don't like the UnderTale reference, the comet one is tied with the green fog suggestions as my favorite because they each have an apparent influence on the world's characters, in this case enemies. I like the Spiky Juice Hair Moon's effect, but the aesthetic itself would be an eyesore; maybe a toned-down version wherein the moon is dark but has oily rainbow colors.
They would also be very moving to look at, at least as I imagine them:
1. The comet streaking across as you fall, or when we look up to the sky for the first time, would offer a sight of splendor and beauty to hint that this choice of ours to run away from an overly cruel teacher may have been the right choice- and that there are sights and phenomena she was trying to deny us.
However, I need to acknowledge that as I've typed this, the appeal of the comet goes entirely to aesthetic, as an event triggered by escaping from Juice School, for the reasons listed above. I concede that your idea is probably to have it just be a random event that could occur anytime after, not specifically as a cinematic backdrop to the escape like I've imagined it.
2. The 'Juice Moon', if I may simply call it that, even with the suggested adjustment, would still be unnerving to look at, and from a gameplay perspective it would be surprising and unnerving to see what a Pollywog is like as a credible threat.
3. The fog would be refreshingly organic, yet eerie; and its allowing frogs outside the swamp biome would really help to make the world feel alive and that these peculiar creatures still follow a logic of some sort.
The meteor one seems underwhelming in my opinion- at least until there's a *whole lot more* to do up that high- and the yarn one seems like missed potential, only aesthetic when the yarn could serve some gameplay purpose and/or hint at new story/worldbuilding elements.