You should be able to use the instant_articles_after_transform_post hook to manipulate the article after the basic transformation is made using the main post body.
Something like:
use Facebook\InstantArticles\Elements\Video;
add_action( 'instant_articles_after_transform_post', function ($ia_post) {
$instant_article = $ia_post->instant_article;
$post_id = $ia_post->get_the_id();
$video_url = get_post_meta( $post_id, 'video_url', true );
$instant_article->addChild( Video::create()->withURL($video_url) );
} );
Does that work?
