If you want less motor noise, you can choose a silent stepper driver like the TMC2100...
On AVR systems you can not get exact timings. You can come pretty close which is what we do. But if interrupt is blocked the stepper interrupt also gets delayed accordingly if it would normally fire. Also on fast speeds you get double and quad stepping meaning it groups 2 or 4 steps instead of having identical gaps between them. This is just because the speed is not good enough. Up to 10000Hz it is ok. With a due you can have exact timings until 100KHz without problems and there interrupts have priority and stepper has the highest. But until now all printers had no problems with timings even if they are off a few microseconds or being grouped.