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I'm not sure the conclusions follow from the premises in this piece: 3D printing + miniaturization + Moore's law (eventually ubiquitous computing does not necessarily yield 'the Matrix.' Combining trends in technology this way is a bit sloppy reasoning, IMO.

What the author is hinting at (eg when he talks about machines the size of blood vessels), but does not say explicitly, is indeed that an era of molecular manufacturing, computing and construction looms. The field of nanotechnology will pioneer these breakthroughs over the next few decades. For further reading I would recommend Drexler's seminal "Engines of Creation" (non-fictive) alongside Stephenson's "Diamond Age" (fictive/scifi).

I think until you can make objects out of super strong material that yet somehow you can easily manipulate in a 3D printer, there is going to be a crippling technical limitation.

But it will always be useful for prototyping.

Now in 100 years if you can print something molecule by molecule out of titanium, well then society is either going to become insanely great or insanely warmongering since it can build horrible weapons and surveillance machines like candy. Given human tendency, I fear for the latter, there is too much profit from war.