Don't worry: this is exactly what Wimsatt is saying. Mechanistic/analytic models are powerful (and necessary, in fact) to do science.
What he criticizes is "nothing-but-ism," when the machine model becomes reality.
This is Whitehead's fallacy of misplaced concreteness: mistaking the abstract for the real.
I'm not surprised that engineers are aware of their models' limitations. Engineering is all about staying within margins after all.