I think you are misunderstanding the feature. Dark mode makes your OS tell all UI to show in a dark color scheme if it has that option. The websites are just doing what you are asking them to do.
What you want is light mode but to use a dark theme on your native UI. You can easy change that in GTK and QT and I remember it was possible to do in older versions of Windows. That will not change the prefers-color-scheme in your browser.
> Users often use dark theme to distinguish UI from content, not blend content with UI.
Err, no. I use dark theme because I like dark themes. But I do think the OS should give you more options, like multiple colorblind modes like some modern video games do.
What you want is light mode but to use a dark theme on your native UI. You can easy change that in GTK and QT and I remember it was possible to do in older versions of Windows. That will not change the prefers-color-scheme in your browser.