Pref Partner Perks are valid on all rates available to the general public (ie you can't stay at The Four Seasons Toronto on the Citibank rate and get the perks). If the package includes breakfast already, then the upgrade and additional perk (lunch, spa, wifi etc) is still valid. If the package includes some lesser form of breakfast (ie no room service) then a pref partner agent can "upgrade" so to speak.
YMMY depending on a few different factors....
Thanks, ABG. I am pleased as punch to stand corrected. It must have been a slight glitch with the FS Vegas property in regards to their special package that they were offering this summer.