The Stair Tool in Revit, simply doesn't work. Revit programmers have perpetuated the error that stairs start at the first nosing and terminate in any flight under the top nosing. This inevitably means that handrails are completely wonky and the stair section is then an embarrassment to show to the craftsman who must build it. In 2D Autocad work, i always design stairs in section and project the plan from the section.
Stairs are ultimately a mathematical problem that use trig formulas in order to calculate. Stairs need to be designed to include the full length of the stair run so that Handrails and guards resolve cleanly at landings. Stairs should use "spring-lines" to start and stop, rather than nosings. The attached fairly complex stair section drawn in Autocad, illustrates how the stair ought to be laid out. if the correct start and terminations were used, Revit might almost be able to model stairs faster than I can draw them in Autocad.