moving blog posts to /blog/ is pretty easy and you can use WordPress settings to do that – no coding needed.
The problem you will have though is that after moving posts, your CPT URL structure will conflict with URL structure of pages – so you’ll have to modify your pre_get_posts function.
As for your post_type_link you can simplify it a lot (if it is not hierarchical… is it?):
add_filter( 'post_type_link', function($post_link, $post, $leavename) {
if ('custom' == $post->post_type && 'publish' == $post->post_status) {
$post_link = site_url("https://wordpress.stackexchange.com/") . $post->post_name ."https://wordpress.stackexchange.com/";
}
return $post_link;
}, 10, 3 );
And I also wouldn’t use pre_get_posts for selecting proper posts. Using parse_request is a lot easier for this task and it allows you to prevent 404 errors a lot easier.
add_action( 'parse_request', function ( $wp ) {
if ( ! is_admin() ) {
if ( array_key_exists('error', $wp->query_vars) && '404' == $wp->query_vars['error'] ) {
$custom_post = get_page_by_path( $wp->request, OBJECT, 'CUSTOM' );
if ( $custom_post instanceof WP_Post ) {
unset( $wp->query_vars['error'] );
$wp->query_vars['page'] = '';
$wp->query_vars['CUSTOM'] = $wp->query_vars['name'] = $wp->request;
$wp->query_vars['post_type'] = 'CUSTOM';
}
}
}
return $wp;
} );