There is a simple change that needs to be made in the stair-by-sketch editing tool.
When creating a stair by sketch you put in boundary lines, riser lines, then finally a stair path. I place all the riser lines where I want the risers to start.

After finishing the sketch and while all the visibilities for a stair are on it looks like this.

You can see that now the solid lines are in the same place they were when I created the stair and now we have the hidden line. This is just incorrect. The hidden line is now showing the riser line and the solid line is showing the tread. Note that I placed riser lines where we are now showing tread lines. This is further shown by the elevation of the stair. We see that it is in fact the treads that line up and not the risers. We can also see this difference when changing the visibility settings and turning on and off the riser and tread lines.

So when I am creating a stair by sketch and placing riser lines, I am actually placing tread lines.
I should be able to place riser lines while editing the stair, then have the riser lines in the same place once I've finished editing the stair. The tread lines would be the lines offset from one another.