Nanoscale technologies are not typically general-purpose. They may make a medicine, or a material, or a small structure with a specific purpose. But if you want to do a different thing, you have to invent a different technology, or combine several nanoscale technologies using some other process. Molecular manufacturing will be able to make complete products using a huge range of programmable shapes with a wide variety of mechanical properties and functions.
Nanoscale technologies are not typically as high performance as scaling laws would suggest. There are several reasons for this, including: fluid drag and floppy-molecule relaxation time in biopolymer technologies; difficulties integrating nanoscale devices into large high-performance systems; imprecise manufacturing techniques; and other limits on manufacturing, such as the planar nature of lithography.
Nanoscale technologies can't deliver huge amounts of information to the nanoscale, which limits the total flexibility and functionality of the manufacturing process. To handle huge amounts of information requires a processing system, and there are no nanoscale processing systems integrated with nanoscale manufacturing systems yet. Molecular manufacturing would be able to build such systems, which could incorporate gigabytes or terabytes of blueprint information into every product at no extra charge. The large machines used by nanoscale technologies (whether scanning probe microscopes or test tubes) also face scaling-law disadvantages that limit throughput.
When all these disadvantages are added together, it becomes clear that, however impressive the results achieved by nanoscale technologies, molecular manufacturing will be far more capable -- at least in its domain of engineered nanoscale machinery integrated into large intricate products.