My understanding is that back in the beginning of the program the original flap setting for takeoff was 15, and the number 1 airplane did not have a yaw damper installed. Somewhere along the line it was decided that since the certification work was done with no yaw damper it had to be flown that way.
Flaps 5 data was obtained later, in another airframe, with the yaw damper on.
With regard to the -300, I believe that the #1 airframe was plugged and used for the aerodynamic parts of the certification, so the same issue carried into that model.
Or so it was explained to me long ago by some folks in Downsview.