>When I calculated the strength of a beam in a thrust reverser I didn't understand the individual molecular interactions, I didn't need to know if the metal was of a body-centered cubic crystal structure, etc. But this is because I was able to apply well-understood and rigorously accepted simplifying assumptions that were conservative (from the point of view of a factor of safety), and fully encapsulated all the understanding I needed to produce a part fit for use.

While I fully agree with almost everything in your post, this sounds an awful lot like an abstraction to me. Perhaps the different between creating software and engineering based on the physical sciences is the degree in which the abstractions are understood and rigorous. Perhaps software engineering is simply in its infancy and may eventually lead to more rigorous designs with less or no bugs in the future?