I reckon if you need an encoder to verify the position of a stepper you aren't using the stepper properly or you are using a stepper that is not powerful enough for the application. Maybe you need reduction gears in place of microsteps.
The whole point of using a stepper is being able to rely on the steps to give the correct position.
Most applications will also have switch (microswitch or optical detector) to identify the HOME position and allow the code to know when the stepper is physically at the ZERO step position.
...R