You can control only one stepper per timer with this method. Thats a bit ineffective. You can control several steppers with one timer if you create the pulses in the ISR.
My MobaTools library does so and can control at least 6 steppers with one timer ( timer 3 on a Mega ). And you can change any parameter ( speed, target, acceleration ) at any time from within the sketch. And you are free in defining the stepper pins.
Maybe there are some restrictions that don't allow this lib in your sketch. But you should consider creating the pulses in the ISR and control several steppers with one timer. That will be more flexible.
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