Yudkowski wanted to break it down to the culmination point that a single collaborator is suffient. For the sake of the argument it is understandable. From the AIs viewpoint it is not rational.

Our supply chains are based on division of labor. A chip fab would not ask what a chip design is good for when they know how to test. A pcb manufacturer needs test software and specifications. A company specified on burn-in testing will assemble any arrangement and connect it even to the internet. If an AI arranges generous payments in advance no one in the supply chain will ask.

If the AI has skills in engineering, strategic planning and social manipulation, an internet connection is sufficient to break out and kickstart any supply chain.

The suggested DNA nano maker is unnecessarily far fetched and too complex to be solved in such a simplified 5 step approach.

I think it will prove computationally very expensive, both to solve protein folding and to subsequently design a bootstrapping automaton. It might be difficult enough for another method of assembly to come out ahead cost-wise.