Replicating toolboxes. Or self-replicating benchtop factories.
Microcontrollers could be produced using dip-pen nanolithigraohy, or a few other techniques.
Of course we need decent open source atomic force microscopes first.
There will always be components that can't be produced on that kind of scale. In reprap parlance we call the "vitamins". An apt metaphor.
This applies to CPU's too and is in no way mitigated by FPGAs.
I use my computer to graph equations. This eliminates the central manufacturing of graph paper; when I want graph paper, I tell my computer to turn into graph paper.
I use my computer to make telephone calls. This eliminates the central manufacturing both of telephones and of telephone switches; when I want a telephone call, I tell my computer to turn into a phone, and it turns routers into phone switches.
I use my computer to watch pornography. This eliminates the central manufacturing of porn VHS tapes; when I want a porn video, I tell my computer to turn into a porn video.
I use my computer to store books. This eliminates the manufacturing of bookshelves, although to be fair, bookshelf manufacturing has never been as centralized as computer manufacturing.
I use my computer to do engineering design. This eliminates the central manufacturing of drafting tables, slide rules, and pocket calculators.
I use my computer to find out what time it is. This eliminates the central manufacturing of wristwatches.
I use my computer to send letters such as this one. This eliminates the central manufacturing of envelopes and postage stamps.
I use my computer to find out about Syrian children drowning in Turkey. This eliminates the central manufacturing of newspapers, although again, this may not have been as centralized as computer manufacturing is.
Perhaps this can help you to understand in what sense the original statement is true, as well as the sense you've already pointed out in which it is false.
This is feasible even using current production techniques. Just make smaller tools.
Open hardware designs are a bigger part of the problem, IMO.
If the LHC stuff pans out, we may need open source replicators. :)