Step/dir driver is correct. To be specific, it is the Stepper Online CL42T closed loop stepper driver. The drives incorporate optical isolation of the Step/Dir/Enable inputs as well as the Alarm output. In order to mitigate any voltage drop issues by running the Arduino output pin through two opto-isolators, I've decided to place the step pin for each motor driver on its own pin. The calculations work out in that I should be able to run two drivers from the same Arduino step pin, but out of an abundance of caution... 
True, I could likely get away with a shorter pulse, and I contemplated using short pulses at the beginning of this project. However, the stepper drives recommend a 50% duty cycle, and there is a minimum pulse width specified (2.5us), so I figured the "output toggle" option would be perfectly applicable to this application. The "one interrupt per step" feature would be nice - currently, I'm checking the pin level every time the interrupt is triggered, and only reacting when the pin is HIGH, which leads to a lot of unnecessary interrupts.
When you mention using both OCR3B as well as OCR3A to generate the short pulses, how would the registers need to be set up in order to get this behavior? I cannot seem to wrap my head around what would be required to get the same pin to be affected by two different OCR registers. It seems that only the OCRnA register is compared when using CTC mode. Am I missing something there?