Chrome already has a setting to change a specific website's color-scheme, although it's only working when Developer Tools is visible (then with Cmd+Shift+P "Toggle CSS media feature prefers-color-scheme"), so CSS implementation actually follows respecting UA-level preference over OS-level setting.
But again, Chrome doesn't have a feature that lets users to choose which color-scheme they want to browse the web (so there is no bug, but it's a UX issue because their Appearance settings doesn't make it clear to the users what this setting changes) other than the setting they gave to developers. Honestly I would love to see all browsers have an option for how color-scheme settings should apply to websites.