After framing, tape off the bottom of the treads. Make a cardboard template and cut some sheetrock - install, tape, texture, prime and paint, then cut away the tape... Fits perfectly.
The other alternative is to rabbit the underside of the treads 1/2" and let your wallboard into the rabbit. Then, the only real problem area is meeting the risers.
For wood, I'd extend the riser and rabbit both the back of the riser and bottom of the tread so any variance is hidden in the rabbits. If you're building stain-grade stairs you probably have better techniques.