I just had the exact same issue. You have to include the editor in the supports argument array to get custom mce boxes to show.
I solved the issue by hiding it with CSS:
function move_posteditor( $hook ) {
if ( $hook == 'post.php' OR $hook == 'post-new.php' ) {
add_action( 'admin_print_footer_scripts', 'remove_edit_div' );
}
}
add_action( 'admin_enqueue_scripts', 'move_posteditor', 10, 1 );
function remove_edit_div() {
global $post;
$post_type=get_post_type( $post->ID );
if ( ( $_GET[ 'post_type' ] ) == 'custom_pt_name' || ( $post_type == 'custom_pt_name') ) {
?>
<style>#postdivrich { display: none; }</style>
<?php }