edit: sorry, I just realized you actually used a stair tool. fixing my original post accordingly.
You are correct in realising that you can't align textures on a stair element. A workaround for this is to simply edit your material, and rotate it to the degree you desire in its settings. You will have to play around a little, since I haven't exactly understood the way the stair tool interprets this rotation value.
As for assigning a different material to the end, this is indeed possible.
There is a way to assign different materials to the different parts of the complex profile. For example the wall part of the stringer could have a brick material and the top part wood. However this is a little more difficult to explain in text, so let me know if this would be useful to you and I'll be happy to create a small walkthrough video for you.