It could be done with :indeterminate state (so key in a cookie would be absent or removed when switching), but I'd probably would do it with radios instead

Note that a checkbox's indeterminate state can only be set via JavaScript, so that lessens the elegance of a CSS-based approach.

I agree that using radios would be better. Or just prefers-color-scheme, which sidesteps the FOUT issue that often occurs when storing theme settings in localStorage.