Its a little known fact that the manual was actually written PRIOR to the game being conceptualized. 

"But how the hell did they do that?", you ask.  I don't know because I'm not a physics major, but rest assured it was done according to that timeline.  So things in the manual that don't appear in game are possibly left out for many reasons.  Perhaps they simply forgot, or maybe they were stoned.  Maybe its a hidden feature of the game that no one has unlocked yet, or could it be they are just screwing with you?  I don't know these answers, but I like to ask pointless questions.  I still contend that the printing company they used to make the booklets forced them to shorten it to its current number of pages.  So they hired a chimpanzee to fling poo and any of the pages hit by said fecal matter were editted out.  Its a good theory, run with that one.

On the flip side of this, there are things IN the game that are not in the manual.  This is due to that weird guy in accounting that Stardock fired last year because they found out he was sneaking in at night and adding content to the game.  But you didn't hear that from me, keep it on the downlow.

As to the econ resources being more rare than any of the others, I think its split pretty equally amongst all the different types.  But econ and military are definitely the best ones to hoarde, at least in my opinion.