Matt, I'll have to take a look at this. It certainly looks odd but I've built it before but I don't remember it clearly.

Matt, Here's my suggestion. It does seem that the long part of the stairway is 7 or 8 boards too long. Cut the upper landing off and install it as indicated with a setback of about 1/8th of an inch. Fold the bottom landing as indicated and fold the stairway. Glue that into the exterior wall with a similar setback (to taste) but let the extra length overlap the upper landing inside the structure where it wont show. Better too long then not long enough. We will correct this on future versions.