Yes, you're absolutely correct. Capacitors in series combine the same way resistors do in parallel. Similarly, capacitors in parallel combine the same way resistors do in series. So, two 10,000 uf capacitors in series will give 5000 uF,in parallel will give 20,000 uF.
"That said, I'm not sure total capacitance even matters that much in a power supply." - It matters VERY much, if you don't want your output voltage to sag during the low phases of the AC input. Too little capacitance will result in output voltage ripple. The higher the current, or the lower the capacitance, the larger ripple. On a stepper motor, that will lose torque, and top speed, and could, in extreme cases, cause the stepper driver to misbehave.
Regards,
Ray L.