It is misleading to consider a cell a factory, because the principle product of an organism is itself . This is not only because it self- replicates, but because its whole endeavor is to maintain its existence and identity. As it own intentional system, it is only incidentally an instrument of human intention. It is not a tool, except in the way that nature is presently managed for human purposes. As long as the process of fabrication is understood in the traditional sense, we are on familiar ground.
Thought is an approximation, and never encompasses the whole of physical process.
There can always be an unforeseen and perhaps undesirable by-product, simply because thought is simplistic. But any technology that truly imitates the wisdom of Nature will necessarily be out of human control. Like organisms, these could only be controlled indirectly. It is quite another thing to imagine tiny factories fully programmable from the macro level. But this is no one-way directive from an external source of intelligence.