page 49 in the report:
"These performances showed a take-off margin of 300m, but this distance
takes the whole runway length into consideration. In reality, the aircraft
lined up at the B1 intersection, shorter by 300m. The crew was under the
impression they started with a positive take-off margin, while this margin
was reduced to zero."
So they performed calculations for the whole runwaylength, but lined up at an intersection.