This will be fascinating to see in practice, with ghostty for example shipping these changes! I expect that the concern you have here will largely be for naught, with some exception. What are some terminal apps you think might be affected, what are test cases?

I didn't read in fully, but what I was thinking in my head is not that we would just totally replace the rest of the colors with arbitrary palette. But that we would sub in better versions of the palette that also used user colors as the base. What was magenta is derived from what the user picked from blue and red.

There's always been such tension between design/creative and users. Apps & designers want their own brand identity, want creative control to make things just so. And are willing to throw user preference & desire on the pyre to get that exacting control. Personally that was always rubbed me extremely the wrong way; I would way rather allow some weirdness & funkiness in, if it leaves the user in control. But I understand the risk aversion, understand the Murphy's law corporatism that makes people and companies want to build strong laws that forbid anything but strictly approved systems, for fear that things go wrong. I understand. But I also things that's a dogshit world to live in.