I find your view somewhat naive. I've been involved in multiple space projects (some very big ones), although never with NASA. But through my interactions with NASA and JPL scientists and engineer, I doubt that the situation there is any different than the one with the agencies I work with.
We are speaking of purchasing organizations run by politicians. Not scientists. How often have I seen scientists and engineer sake their heads on the attribution of a contract or selection of a mission? I stopped counting when I ran out of fingers to count on.
The attribution of the contracts is highly dependent on geographical distribution rather than on expertise. The selection of wrong contractors, based on geopolitical motive, costs years in delays and millions in over costs. It magnitude over the interaction you describe. If only that was the only source of higher costs...
The selection of the projects or mission that get financing is even worse. It became a real political farce, and is undermined by political marketing (eg. what sells well to the people financing the agencies) and by the true role of these agencies: financing the aerospace industry.
I would answer in short that people who assert things like you do haven't been in the business long enough or have been doing so with their eyes and ears closed. What you describe is entirely correct, but accounts only for a minute fraction of the cause of the high costs found in the space industry.