But none of that was configured in one place, with every other program taking its lead from that central configuration. Instead, effort must be made to work through every program individually, customizing its color scheme.
that's how it has always been. There isn't a system out there that does theming where some apps won't be left out. It's practically impossible. Even dark mode on iOS doesn't work on every app. And then there is Android... which is just unspeakably bad at all things UX.
it still is, just look at how neat things in https://reddit.com/r/unixporn/ look