I have switched our logo from $wgLogo to
$wgLogos = [ 'svg' => ".../wiki.svg", 'icon' => ".../icon.svg", 'wordmark' => [ 'src' => ".../wordmark.svg", ], ];
WikiSEO now sets the default image as the /w/resources/assets/wiki.png instead of the appropriate logo. I'm not sure if this is because WikiSEO doesn't understand $wgLogos, or if it doesn't want to use an SVG.