I think I'm still missing something... The GNDs to the right side of the OP can all be connected together, is that right? Does the attached corrected schematic look ok?
Schematic is correct with the exception that you missed the ground on the opto transistor emitter. Connect that to the other gnd points as you've done and you're good to go.
Could the Arduino PWM output be a problem for the motor controller since it is not really 0-5V, but 0 or 5V?
No, because the circuit from Hackaday converts PWM to a 0 to 5 volt analog value. It also provides the required isolation. Without the isolation, you'll probably blow up your Arduino and the USB port in your computer since the Bodine drive interface floats above ground by an unknown voltage level. Without isolation, you'd create what's called a ground loop which results in undesirable and sometimes uncontrollable currents flowing in circuits where it should not.
I don't think that cd4049 circuit will give you clean dc output, it's a function of the input impedance of the drive which is unknown.
A digital pot will cause a ground loop between the Arduino and the drive. You could use one but you'd need an I2C isolator like the ADM1250
I'd be tempted to look for a +5v on the motor board. If you are lucky, you avoid having another power supply and regulator etc. for the isolated analog output circuit you are adding, but here you have to know what you are doing.
That's tempting but it wouldn't work without redesigning the circuit using using rail to rail op amps. The schematic you drew in post #5 will a-okay with the 12 volt supply shown, you just need to connect the emitter of the opto as previously mentioned.