I feel the opposite. If the hardware/setup is accurate the stitching process will be flawless. Might want to invest in a ZigAlign.
If you can get the mechanics right, stitching will be simple, and could be done in PS.
To avoid having to scale, make sure the distance to the subject is the same (and do not re-focus).
To avoid distortion make sure the lens is perpendicular, and the sensor parallel.