Well, lightbox only shows (or rather, should show) only when You select link to media file. If you don't, no lightbox. Simple as that. It works that way in foobox and 'Responsive Lightbox & Gallery', probably most commonly used addons. Or a simple checkbox would suffice (and default settings for lightbox in theme options). I read the page you linked, but it doesn't say it doesn't work traditionally, with just a link to media file. I thought it's just a description for people wanting to use shortcodes, which are sometimes handy, for example when you want to use lightbox in a specific way.
Once again, I am extremely disappointed, it's not only lightbox, but most of other elements are incorporated into the theme in a way, that nobody will be able to use them. There are no tools whatsoever to help the editors and not using coding.