What exactly does (Cleaner, Applications tab, Firefox/Mozilla) Site Preferences clean? I tried to find it in the help section but this particular subject is missing in the help topics. If it does exactly what it alludes to then it cleans any preferences you may have set for each particular website, such as allowing scripts? Is this correct?
If you clear the site preferences then the Firefox default settings will be used.
From your 2nd link:
Clearing "Site Preferences" clears all cookies, images, pop-up windows, software installation, and password exceptions.
Information from the 1st link sounds more disastrous than the 2nd, if you have unique settings selected you definitely would NOT want to choose Site Preferences. Subject of the 2nd link sounds redundant for CCleaner since all of those are already cleaned with the other options, unless I'm mistaken.