@Curanthir The story hasn't even gone off the rails at all. If I had to explain it simply, Cairn and Achema's relationship is an allusion to a Buddist story. In fact, one might even say that Phos' journey is in fact just Phos' journey to reaching a certain nirvana or understanding. Such that he is able to bring peace to everyone; the slugs, the lunarians, and all of the gems. This would be Phos essentially taking Sensei's role but on a much grander scale where he literally becomes the Land of the Lustrous. Or he literally turns everyone to nothingness and achieves Nirvana for everyone. Ichikawa seems to also note that a lot of the story was inspired by her time learning about Buddhism.
See image describing how HnK relates to buddhism here: https://i.imgur.com/G1zp8FV.jpg
Here are 2 images relating to how Cairn is an allusion to Rohini from Buddhist legends: https://i.imgur.com/VwlN78c.png https://i.imgur.com/GTtg5Gp.png
Here is another image theory showing the connection between Achema and Chandra from the Buddhist legend: https://i.imgur.com/9zpr8pP.jpg (You'll want to focus on the /Om Manipadme Hum/ section)
Here is a link to a bunch of the lore rants regarding Houseki no Kuni and its several different allusions and lore:
https://imgur.com/a/3fVKI1A