Where are the good docs?
I believe that you’re not asking in the wrong place, you’re really not asking a question. What you define like “The Good Docs” is completely subjective. The guide you linked clearly says: 


  Important: This document is intended for use by security
  professionals in sensitive
  environments. Implementing the
  techniques and settings found in this
  document impacts system functionality
  and may not be appropriate for every
  user or environment.
  
  If you’re using this guide, you
  should be an experienced Mac OS X
  user, be familiar with the Mac OS X
  user interface, and have experience
  using the Terminal application’s
  command-line interface. You should
  also be familiar with basic networking
  concepts. Some instructions in this
  guide are complex, and use could cause
  serious effects on the computer and
  its security. These instructions
  should only be used by experienced Mac
  OS X users, and should be followed by
  thorough testing.


So clearly these “good” documents are not that good for everybody. In any case,
Spotlight doesn’t index /System because that could be a security problem on its own (it would need permissions to do that, a set of permissions that you don’t want to give to a userland daemon running all the time, with access to a UI). Why would a regular user want to keep an index of /System remains a mystery to me, it only has things that are for the System and not for the user to find and manipulate. 

You can, however, use the terminal to touch that if that’s what you want, but no user should ever attempt to land in /System, it can only break so many things…

Where did you get the idea that 


/System is the most important place to keep an eye on files ?
Spotlight is a tool to keep an eye on files?


The place to keep an eye on files is in your very own /Users/YourFolder, because that’s all the access you should have (to write that is).

Spotlight is an indexing/searching tool, not a tool to monitor files that may seem suspicious in reserved system places. 

All in all, if you still want those docs, I’m sure that most of them will be available in the developer’s area of Apple’s website.  (developer.apple.com). You can create a free account and start from there. 

On the other hand, if you are a “security professional” then you are using the wrong tools for your job. Spotlight is ok as it is, if anything, you might want to restrict it. I’m sure that if you make spotlight run as root it will eventually index that, but of all the possible ideas that come to my mind, that is probably one of the worst security ideas ever conceived. There’s a reason why root user is disabled by default, there’s a reason for sudo and there’s a reason for normal accounts. Use them wisely, use them in peace.