It's likely a small difference, but the main advantage of having it in the HTML is that it's immediately available, so you don't have to deal with the flash of unstyled content being in the wrong color scheme.

Source: https://css-tricks.com/almanac/properties/c/color-scheme/#theres-a-corresponding-meta-tag-too

The meta tag makes your browser default to dark for a user's dark preference. That means you don't need additional CSS at all for a baseline. It also means if you forget or miss a dark or light alternative style for some element, the browser defaults already cover them.

Thinker mentioned the separate CSS loading separately. Which can lead to relayouts, in the worst cases flashing like they mentioned, but typically just increased loading time until first render, and less robustness against connection issues (html loads but css doesn't).