Question Mark ? not working in URL

I have a url like

site_url('admin/&route=design/layout/edit/' .'&layout_id='. $result['layout_id'])

Generates

http://localhost/codeigniter/cms-1/index...ayout_id=1

With question mark in front of index.php?

But does not let me use the $this->input->get('layout_id');

It happens ever time I add ? does not seem to work with HMVC

I am using codeigniter 3

$route['admin/&route=design/layout/edit/(:any)'] = 'admin/design/layout/edit/$1';

Note:

I do not want to use

$config['enable_query_strings'] = FALSE;

$config['controller_trigger'] = 'c';
$config['function_trigger'] = 'm';
$config['directory_trigger'] = 'd';

Any suggestion why cannot use ? after index.php seems strange that will not allow me to use that and let me get query.

Options +FollowSymLinks

Options -Indexes
DirectoryIndex index.php
RewriteEngine on
RewriteCond $1 !^(index\.php|images|robots\.txt)
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?$1 [L,QSA]

There's only one rule - please don't tell anyone to go and read the manual.  Sometimes the manual just SUCKS!