Battery Wiring - 3 Independent systems with common ground
It's not only okay to connect the grounds together, it's mandatory if you want them to communicate or interact with each other in any way. Without a common ground reference, what you have is several entirely separate systems, and any communications between them would have to be isolated using something such as an optoisolator or a transformer.

Charging one set of batteries when they all share a common ground is also no problem.

That said, you really don't need separate batteries for different parts of your system, whatever the motor controller manual says. At worst, you will need separate regulation for high-noise parts of the system, and input filtering (such as LC circuits) to reduce noise from the motors. Just look at something like the Tesla- you don't see that having several different battery banks for different parts of the cirtuit.