The way the video describes such a machine would be so impossibly impractical. Moving parts are a nightmare to deal with, one little breakdown of any of those nanoscale moving parts would cause the entire thing to stop working correctly.

A more practical design for a nanofabricator wouldn’t brute force atoms together with nanoscale factory machines, but would instead use precision lasers to both breakdown the starting molecules and as a catalyst to overcome the potential energy necessary for atoms to bond in a particular configuration.

Not even to mention the scaling issue with the machine approach, with precision lasers, it’s infinity more scaleable and to scale up all you would need is more lasers that work in coordinating.