I'm not sure about the scalability of mechanosynthesis, either (Massive parallelism gets thrown around a lot, but there may be something to convergent assembly) , but I was just talking about the basic tip chemistry.

Zyvex has a similar process called Patterned Atomic Layer Epitaxy which seems more promising as a large-scale manufacturing technology, but I have not seen designs for nanofactories of megadalton-scale products made using PALE.