If you look within those pyramids you'll find that most of the time the innovations that made the larger pyramid succeed were the result of small, focused teams. For instance consider the famous aircrafts designs for the U-2, the SR-71 Blackbird, the F-117 Nighthawk, and the F-22 Raptor. Large pyramids, right? Wrong. All were the result of small teams at Lockheed under Kelly Johnson. (Who had a famous list of rules for successful projects, the third of which was, The number of people having any connection with the project must be restricted in an almost vicious manner.)
Was this unusual? No! You brought up putting men on the moon and Space X. Both were utterly dependent upon the efforts of a small community of people studying liquid rocket fuels in the 40s-60s. What kind of people were those? According to http://library.sciencemadness.org/library/books/ignition.pdf (that copy didn't load for me right now, but http://web.archive.org/web/20121013085952/http://library.sci... did) there were at most 50 men scattered across multiple companies who understood the field, all of whom were "howling individualists".
The same is true in computer science. Major projects with huge impact created by a handful of people. Examples include Lisp, Smalltalk, C, Unix, patch, emacs... Companies which, when you tear back the curtain, truly were dependent upon very small numbers of people. Ask anyone who follows tech if Apple would have been Apple without Steve Jobs. Ask anyone who has worked at Google whether Google could have become Google without Jeff Dean.
Large groups working together on a known goal are essential to our society. We could not have the world we have today without them. But find me an example of great engineering that requires those pyramids, and when you tear back the curtain you'll find in technology after technology, in component after component, that critical pieces were absolutely dependent upon small groups of people. And those people, far more often than anyone in charge would like to admit, were rule breakers.
Those rule breakers who were the ones who got things done are, for technologists both then and now, heros. You may wish that the world of technology was better behaved. But you cannot understand or appreciate it without accepting the fact that it really is that messy.