If you enable this option, the links generated by the system will not include "index.php?". However, to enable this, mod_rewrite must be available and an appropriate .htaccess file must be in place.
Which I think is absolutely fine. I think it could be made perhaps even better if something like "For configurations across various web server setups (II7, Apache etc.), refer to the XenForo manual."
I say so because I tried enabling the Friendly URL option, but in vain since I had to put a web.config file on my server, and only came to realize that when I myself checked the manual where it was all explained so nicely and in detail. Perhaps a link given right there would save some time.
Just a suggestion.