Thanks for logging all of this, @j127.
I’m able to reproduce the issue of the Horizon and Horizon Dark palettes automatically being re-enabled after a site rebuild, so I have logged a bug for that. We’ll have that fixed up ASAP.
Aside from the knock-on effects from that bug, the other things you noted all seem to be related to the default dark mode color scheme id setting. The good news is that we have an update in the works that migrates that setting into your theme - this makes it much more usable, easy to find, and less prone to inconsistencies like this. We plan on merging that update within the next 24 hours, and will have an announcement and docs to provide more details. I’ll circle back here once it’s live, and then you can test it out to see if it remedies these issues for you.