When I initially load a site, the theme color seems to be determined by the favicon even if a theme-color meta tag is present. But if I then renavigate with the same site, or even just Ctrl-Tab to another Vivaldi tab and back, the theme-color from the meta tag is then applied.
Since this is the only direct question like this I've seen on the forum, I'd like to complete it by providing an answer. (maybe change the post title? ie "Theme accent / tab color"?)
This is the default behavior of a Vivaldi theme. In order to override this you must customize the theme and uncheck "Accent color from active page" thus using a custom theme.
You might have to click the "pen icon" again to save your changes, but this will cause your chosen accent color to remain static regardless of what page you visit.