Cells are naturally occurring microbots with nanobots as organelles. They use enzymes as catalysts and pay close attention to chirality. All cells are by default molecular 3D printers.
Yes living cells at standard temperature and pressure most certainly can synthesize graphene graphane carbon nanotubes carbon nanothreads and so on. Cells already have atomic precision. Our technology does not have atomic precision which is why we use brute force methods of really high pressures and temperatures.
I highly doubt such a mechanism would evolve, but it most certainly could be designed.
It wouldn't work well for collagen. Graphene works well as a conductor. Nanotubes work well as reinforcement in a composite.
Nanothreads being sp3 bonded can be scaled to macroscopic quantities while maintaining it's properties and be good for muscles. The muscles would still need heat ions or electrostatic mechanisms to work, but it's the nanothreads that will be deformed to make the muscle move.
Collagen is meant to be elastic. A hard somewhat elastic composite can be made, but if all your looking for is toughness then have subdermal scales overlapping and held together by something similar to collagen. The skin would still be skin, but underneath would be super tough scale.
Ultra high molecular density slider silk or an analogue to that could replace collagen and would be superior, so long as it interconnected in the right way. They can be reinforced with graphene without being entirely graohene.
Kevlar threads are tough, but it's the way those threads are connected that makes them effective as armor.
Everything reacts with something. Even golf with the highest corrosion resistance can be dissolved. Once an element is at the atomic scale,it can be built. Forging steel will always be simpler then using cells or nanobots to atomically print it one atom at a time, but those cells will still be able to do it.
Hope this helps.