Why not make a custom shaped stair using a fill to define the shape, and a line to indicate direction.
- Use a temporary section across the stair to work out where the stair will intersect the sloped wall at the top, then draw the fill to that point on plan.
- Draw the direction line parallel with the walls to keep the treads at right-angles.
- Select the fill and line, then go to Design > 'Create Stair Using Selection' and set up the stair to your liking. Remember to save it to a loaded project folder.
The stairs should now appear correct on plan, section and in 3d. To neaten the section further you could SEO the wall away from the stair but this detail wont effect the overall shape on plan.
Hope that helps.