I decided to Change the 12 x PWM Hat to use High Side Current Sensors. Below is the schematics of the new sensors. This means I measure current out on each PWM signal.
Using high side sensors actually simplified the routing so it was a straight forward change. The reason I started with low side sensors is because that is straight forward for DRV8313 and more common for 3-phase. It would have been ok for Stepper and DC motors, but it made it difficult to measure current if you used a single PWM channel stand-alone.