Interesting thought experiment, but I don't see why automating machines that build and repair other machines wouldn't be sufficient. At the limit, such a machine would be able to repair itself, or repair other long-running machines. I imagine it would come down to wear and efficiency loss.
Manufacturing requires micromanaging every aspect of the process, requiring special machinery, trained workforce (human or not), inventory management.
Reproduction, once we master its blueprint of course, is much less demanding: just provide the ingredients at approximate proportions and the chemistry will work its magic to provide a similar enough unit to achieve the required task.
In this case I'm seeing 'micromanaging' as something akin to automating a Tesla superfactory: machines complete each individual step, we get a working car at the end.
Obviously, we'd have processes built that build machines for each of the individual tasks, or changing tracks to support new car models.
From my perspective, this framework of a factory could map to many other endeavours where we either produce the end product or a machine used for something else.
So, the difference would be whether the machines utilize chemical/biological processes for working, or are made out of steel, at which point it would boil down to economics.
I guess I don't see what's so special about adding 'bio' to these perpetual factories.