I think I understand... I think you're saying that the center of the universe here, with respect to ground, is the Roboclaw.
Thus connect the main battery only to MB(+/-) on the Roboclaw.
And the logic batteries to (+/-) on the Roboclaw.
And the logic batteries (+) to 5v stepdown regulator, then to the Pi (+).
The 5v regulator's (-) is common to both the logic batteries (-) and the Pi (-).
However, I have already wired everything, treating the external ground bar as the common ground point. (not the Roboclaw's ground plane as the common point; since I didn't know this). (just didn't think about it in those terms).
I think this (below) is similar to what you're saying, but still keeping most of what I have already wired:
1) main battery (+) ---> switch S1 ---> fuse F1 ---> Roboclaw (MB+)
2) main battery (-) ---> ground bar
3) ground bar ----> Roboclaw (MB-)
4) logic batteries (+) ---> switch S2 --> fuse F2 ---> Roboclaw (logic +)
5) logic batteries (-) ---> ground bar
6) Roboclaw (logic -(neg)) untouched since already part of internal ground
7) logic batteries (+) ---> switch S3 --> fuse F3 ---> 5V stepdown Regulator (Vin)
8) 5V stepdown reg (Vout) --> Raspberry Pi (+)
9) ground bar --> 5V stepdown reg (-)(gnd)
10) ground bar --> Raspberry (-)
I think that's another way of saying the same thing.
If so, that leaves one unanwered: the USB conection between the Pi and the Roboclaw. Since I'm assuming the neg(-) of the USB across them would constitute another ground path, thus a loop.
If so, should I use opto-isolation
I want to retain the external common ground bar.
And I don't know that in the future I will stay with using the USB as the communications link.
And I don't want to power the Pi from the Roboclaw. I want them separate , only having a common ground.