No, they aren't opening a dollar store, but the numbers from TFA are enormous. SpaceX and Blue Origin may be standing on a mountain of previous research & tech from NASA, but NASA itself is also standing on that same mountain. Since it is their own mountain, it should be logical that they would be more effective in applying previously discovered knowledge to their new projects.
And, purely the fact that space is a hostile environment isn't a fact that can be used to explain away any level of bureaucracy and overhead. Arguably, the deep see is a more hostile environment because of the higher pressures. Combine that with using nuclear power in subs and you actually have an equally complex and risky environment, probably more. There are a lot more situations where quality control is an absolute requirement, such as nuclear power, (intensive) health care, chemical plants, etc. How big is overhead in those industries?
Probably the biggest problem in discussing overhead numbers for something that doesn't work yet is that you don't have the complete picture yet. If NASA overhead costs, say 10 billion for a total program cost of 15 billion then you could argue that the overhead would be 66%. But if we actually start transporting stuff into orbit and send a bill to whoever is sending the stuff (even if it is an internal NASA team), and you could bill them 10 billion in the course of the program for the time and materials required for the launces, then the overhead percentage would suddenly be "only" 40% (I know I'm taking a lot of shortcuts and most management would probably stick around after the SLS has been delivered).
But, no, simply ignoring these astronomical levels of overhead because of the complexity of space as an environment is in my opinion not valid.