Galvanic isolation in multiple battery design
There is no pointing isolating the batteries unless all your circuits are isolated between the two sides as well. ie. Control board running off battery A and motor driver running off battery B must interface through isolators. Or motor driver that accepts battery A for logic power and battery B for motor power must have isolators on board between the two sides. Isolation takes a LOT of work because of this.
Two unisolated batteries (i.e. sharing a ground) does help with power supply disturbance issues but won't really help with noise issues like isolated batteries will.  Often a single battery with proper decoupling and grounding is the simpler solution for both.
Two batteries (isolated or not) makes sense if your motors run at much higher voltage than your logic because you do not need to step down the voltage. It also allows your motors to run the battery dry but not kill your electronics which can be important in some applications (i.e. a model airplane whose propeller motor uses one battery but the electronics  which include the radio and servo motors which allow you to control the plane run off another battery).
Newbies worry too much about ground loops. Ground loops are only a problem if they cause a problem.
On a tiny 3A robot there should be no good reason to isolate or use two batteries. 50A airplanes often fly with single batteries and no isolation, and those things crash with too much noise or power supply disturbances.
DO NOT regulate the voltage to the motor. Choose the motor and batteries to run direct. It is a waste to try and regulate voltage for high a power system that is not sensitive to voltage like a motor. A motor driver is kind of like a crude regulator for the motor and that is its job so don't make yourself do the same thing twice.