Diagram 2 would be the accepted norm.
Look up the topic of "ground loops", which can often be a serious problem.
How can you not have ground joined? You use plastic bolts to attach the motor to the chassis?Motors usually have rubber vibration isolation mounts but it's difficult to avoid some steel part touching somewhere. That's why most engines have a thick copper ground strap. This ensures any currents have a controlled path to ground, instead of running down the throttle cable and heating it up or causing sparks.