[reitanuki]

I suspect this is a problem for your browser? The CSS media query only makes sense as 'prefers dark webpages' — there'd be no point having it, if it means 'the browser theme is dark and it doesn't matter what the user prefers in terms of web pages'.

Your browser should offer you a setting to choose whether you prefer dark webpages or not (SEPARATELY from the browser theme). Not sure if Chrome currently does but if this annoys you, it would be worth looking for.