Think about all the different things Boeing works on, all the details involved in the design of a modern airplane or spacecraft. How is a third party supposed to audit all that, when the designs are so complex and in such a relatively niche field? The most they can do is look for obvious things and make sure the data makes sense.

The problem isn't that the system is corrupt, it's that you're expecting a third party to both be close enough to be intimately familiar with all the details of the airplanes and spacecraft and yet separated enough from the company they're monitoring to not have conflicts of interest.