The Shop page is actually an archive page for the Products CPT and won't obey the layout settings for the page. This snippet fixes that.

functions.php

<?php

/**
 * Make WooCommerce product archive obey shop page layout settings
 */
add_filter( 'genesis_pre_get_option_site_layout', 'child_do_shop_layout' );
function child_do_shop_layout( $opt ) {
    if ( is_post_type_archive('product') ) { 
        $opt = get_post_meta( wc_get_page_id('shop'), '_genesis_layout', true); 
        return $opt;
    }
}