You have selected the S2 style system...
While this is the reason for the Modify Journal page missing some options, I think it could be worded more clearly. If an S1 user stumbled upon this FAQ whilst looking for something else, being told they're using the S2 system is going to be quite confusing. I propose something like the following (note that I have only change the first sentence of the first paragraph):
If you have selected to use the S2 style system for the customization of your journal, there will be options missing from the Modify Journal page. The S2 style system is not completely controlled by the Modify Journal page (http://www.livejournal.com/modify.bml). Some options, such as the ability to enter overrides, do not exist when using the S2 style system. Please see http://www.livejournal.com/support/faqbrowse.bml?faqid=173 for information on each style system and advice on which style system is the most suitable for use with your journal.
Information on switching your journal between the S1 and S2 style systems can be found at http://www.livejournal.com/support/faqbrowse.bml?faqid=168.