Yes WHMCS works fine with the php functions mentioned disabled. Most if not 99% of the time you will run into ini_set errors (not on whmcs but on various other scripts). If you simply edit out the ini_set from the configuration files or have someone knowledgable do it you won't run into any errors.
To directly answer your question, "you will have no issues running whmcs and most other scripts with all of the above recommendations".
My server runs vBulletin, IPB, PHPbb, WHMSonic, WHMCS, Shoutcast, and many other scripts without any flaws.