All of engineering is a counter example. We have a fiendishly hard time replicating the precise lift mechanism of flying birds (this is still an active are or research), yet we have designed and built the Boeing 787 and SR-71.
Life is an existence proof that atomically precise nano machines are possible, but it is not in any way a demonstration of their limitations any more than birds represent the epitome of heavier than air flight.
Correction: I read up on the story to refresh my memory, and Clippy does use a form of nanobots. I was mixing it up with another story, that just used a timed hyperlethal pathogen.
Life is an existence proof that atomically precise nano machines are possible, but it is not in any way a demonstration of their limitations any more than birds represent the epitome of heavier than air flight.