When I add it to the allowed image types I can upload and link to the pdf file without issue. Here is what my settings look like for the allowed images inside of the config.php file at HTMLEditor > editor > filemanager > connectors > php:
$Config['AllowedExtensions']['Image'] = array('bmp','gif','jpeg','jpg','png', 'pdf') ;
What is the result that you get if you add it here?