Ignore post by meta value in the main query

add_filter( 'posts_results', 'insert_post_wpse_96347', 10, 2 );
function insert_post_wpse_96347( $posts, \WP_Query $q ) {
    remove_filter( current_filter(), __FUNCTION__ );

    if ( $q->is_main_query() && $q->is_home() && 0 == get_query_var( 'paged' ) ) {

        $args_uno = [
            'meta_key'                  => 'caja',
            'meta_value'                => 'uno',
            'post__not_in'          => get_option( "sticky_posts" ),
            'posts_per_page'        => '1',
            'status'                        => 'publish',
            'suppress_filters'  => true
        ];

        $args_dos = [
            'meta_key'                  => 'caja',
            'meta_value'                => 'dos',
            'post__not_in'          => get_option( "sticky_posts" ),
            'posts_per_page'        => '1',
            'status'                        => 'publish',
            'suppress_filters'  => true
        ];

        $p1insert = new WP_Query($args_uno);
        $p2insert = new WP_Query($args_dos);

        if ( !empty( $p2insert->posts ) ) {
            array_splice( $posts, 0, 0, $p1insert->posts );
            array_splice( $posts, 1, 0, $p2insert->posts );
        }
    }
    return $posts;
}

function cmp_exclude_featured_posts($query) {
    $exclude = array();  //Create empty array for post ids to exclude
    if ( $query->is_main_query() && $query->is_home()) {

            $featured = get_posts(array(
                'post_type'     => 'post',
                'posts_per_page'    => 2,
                'meta_query'    => array(
                    array(
                        'key'           => 'caja',
                        'value'     => array('uno','dos')
                    ),
                ),
            ));

            foreach($featured as $hide) {
                $exclude[] = $hide->ID;
            }

            $query->set('post__not_in', $exclude);
        }
}

add_filter( 'pre_get_posts', 'cmp_exclude_featured_posts' );