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The comment by ThatPurpleGuy actually answered my question.
In principle, prefers-color-scheme is not used. JS only detects whether the user is using dark or light mode and then adjusts a class in the body tag. Depending on which class is in the tag (light or dark), different CSS variables are applied.
Here is the link to the YT Tutorial: https://www.youtube.com/watch?v=rXuHGLzSmSE