If you have isolated supplies, you can tie them together at any potential

Ground is a funny term. Is it earth? Or is it common? Or is it the frame?
Not only should the traction circuit be isolated from frame ground, it's best to have a leakage monitor/alarm to insure that they remain that way.
If you are designing one of the circuits (controller, etc), you can implement this with a simple voltage divider. Supply battery voltage through a pair of high value (100K-1000K ohm) resistors safely connected inside the high voltage section. On your low voltage board, monitor each side with 1K-10K resistors as the other half of the voltage dividers. By putting the high value resistor close the source you limit external exposure to the uA range.
Of course if you are designing a smart battery monitor, it's easier. Just put the leakage check on the master controller. It already has to deal with full battery voltage and communication isolation.
Don't expect that your monitor will report absolutely zero leakage. Everything has a little leakage current, including the monitor you just built. It's common for controllers to connect the isolated circuit through to ground through a very high value resistor or a leaky high voltage decoupling cap.
As far as picking the isolation point for the motor controller, that's up to your design. If you have a separate low voltage control and high voltage switching boxes, you might choose to isolate the output of the low voltage box (which protects the control electronics from wiring faults and induced current), at the input of the power box (which prevents high voltage from escaping when power semiconductors drop their "semi") or both.
One simple solution is to use an optoisolated gate driver. The drawback here is that they are a step down in current and speed from the best gate drivers.
For the gate driver power supply, you might consider a "bootstrap" circuit instead of a DC-DC converter module. The average power used by a gate driver is pretty low, and a 20V-30V supply isn't useful for much else, so a sleazy clamped charge pump might be an acceptable low-cost choice.