I mean, the why is explained through the scenes when you take over child Kinu inside the orb, your decisions influence whether your daughter becomes obedient or rebellious. Personally, I haven't played the Hime route yet, so I can only speak for Inari, but in the interactions with Kiyoko afterwards, she very much still loves the Champion and even though she begrudges her daughter's choices and would rather things went differently, there's still a measure of appreciation and sometimes even pride there, even if it is hidden behind vague concessions. Same for Kinu: She still loves her dad very much, but she's resolved to be her own woman, so she distances herself, in the very awkward and clumsy way that teenagers tend to do.
If anything, then these two need time to first get their bearings in a completely "new" world where they don't have to contend with only each other and x younger siblings but with other people, whole socities full of their own problems and expectations, and an active crisis one if not both of the parents need to keep their attention on. Kiyoko has to readjust from not being alone anymore and having to update her values and outlook to current day circumstances, Kinu needs to find her place in a world where having it her own way and refusing to give in has more far reaching consequences than "Mom will be angry" (well, in Inari Kinu's case at least)
If anything, the whole storyline is still ongoing. At least I hope so.