Arduino Zero - Stepper control (interrupt)?
As Stepper::updateAll(); isn't shown I don't know what it does.  For accurate timing it would make sense to use hardware-operated output-compare output pins like TIOAx and TIOBx, instead of running some code to drive the pins when an interrupt occurs.

If you need to control several wires per motor – such that a pulse on a single output line isn't enough – you might consider using a 74HC595 (or other shift register) to transfer the bits.  Thus, each time an output compare occurs, the  TIOAx and TIOBx line would pulse the ST_CLK (store-clock) line of the SR, to transfer bits from the shift chain flipflops to the output flipflops; then, at its leisure the interrupt routine can shift the next set of bits out to the '595, ready to be transferred at the correct moment, when the next output compare occurs.

During stepper acceleration or deceleration, the timer count-limit would also need to be updated within the ISR.