Have you tried to move the stairs (for the moment), add that tile of flooring manually (which should make it normal customizable floor) and then move the stairs back? That might work. I believe it worked for me when I was trying things.
The extra landing square is something that was the case since terrain tools when I built split-level outdoor terraces. After this patch, the stairs work pretty much the same, just with the added corner mechanisms.
In TS3, a staircase took 4 squares (+ landings) so U-shaped stairs took 2+2 (if you went through the cheats and other hurdles to build them). In TS4, they take 3 squares on normal wall height, so we're down to 1+2 or 2+1 which feels a bit strange, considering U-shaped stairs are prevalent in multi-level buildings where I live (offices, universities, apartment houses,...) and they have even length on both 'branches'.
