Check out the diagrams as you scroll down the Northdory page.  They show perpendicular thwarts.  This makes sense.  Since the slots in the thwarts have to slide down and over the ends of the bulkheads, it would be difficult to cut the slots at an angle.  Also, the one thwart gets held in place by the star knobs and bolts.  Again, hard to do at an angle.  When I came to gluing the support pieces (forget the name) to the side planks, I first taped them onto the thwart, lowered the thwart in place, then pencil marked the location of the support pieces.  That helps ensure that the thwarts are perpendicular.