I learned how to do cycle and latency calculations for this puzzle. Quite fun. 

I'm pretty certain that an arm with three rotations is the fastest way to transport a single atom: 6 tiles / 3 cycles or 2 tiles/cycle. If that is the case, then logically, sending the first and second atom in opposite directions and dropping them at the same time as the last atom must lead to the highest possible distance, right?

It can be faster to transport a big stick, but the dis- and reassembly takes precious cycles away again, so I don't think it works here. Possibly in another metric.