If you add a field to the media/attachment field and set it to be a WYSIWYG editor, then click the ‘link’ button in the toolbar, the popup is under the modal.
I know it’s probably a wordpress thing but I thought it best to report it anyway. 🙂
I will mark this thread for the developers attention.
You might also want to open a new support ticket as that might be a faster way to get the developers attention on this bug. http://support.advancedcustomfields.com/new-ticket/