I think the largest issue with this is it is currently a Safari-only, and an early Safari-only release at that. And that the latest MacOS right now is the only major commercial OS offering a dark theme to the extent that it does.
A quick look at Safari's desktop browser market share reveals it to be about 4% right now. When this kind of standard makes its way into Chrome and/or FF, it'll be relevant.
Until then, it's a toy, and nothing more. Nobody could ever realistically expect this kind of thing. It doesn't increase the complexity of web design by that much. If you think adding CSS exceptions for inverted colours is the straw that broke the camel's back on web complexity for you, perhaps you just feel like we should've stuck with the late 90's or worse, early 00's web standards?
Many websites, even YouTube, already have a 'night' or 'dark' switch. It makes a lot of sense, and genuinely is not that hard to implement.