"Most important, an engine must be disassembled bolt-by-bolt to get at the worn piston rings deep inside, then meticulously rebuilt; but living tissues are repaird from the inside by efficient molecular machines." -josh mitteldorf
While this quote deals with macroscale machine of a car, this is the issue I think comes up with bringing traditional machinery to the nanoscale as opposed to using machines more similar to biological ones. In the event of some failure of a traditional machine like nanobot, it would seem repair would entail complex disassembly and reassembly to get at damaged parts, while in machines more similar to biology the molecular machines are more easy to repair or replace with far less effort.
Would complex dis-assembly and reassembly be suitable say within a human body? Would the damaged traditional machines have to move to a repair zone to be repaired? Is this at all viable? What about in places with harsh radiation that may damage molecular components? Some lifeforms are very resistant to radiation, and can repair vast damage, could a more traditional machine scaled down do the same?
It seems to me that the easier to access and repair way in which molecular machines are handled in biology is an optimal one, which allows for self-repair and indefinite maintenance unlike traditional machine designs. Using synthetic biology novel molecular machines can be added to the natural repertoire allowing for never before seen functions to arise. Ideally the combination between information technology and biological technology may yield a new kind of machine able to manufacture almost anything imaginable.