We operate to Nett Performance standards which are significantly factored for safety from flight testing performance and Gross performance. If they had calulated correctly, stopping at or below V1 should not have ended up with a 400m over run. There is also a factor of safety of 2 seconds built in for recognising an Engine failure at V1 to abandoning the Take Off.
Under FARs and, I believe, JARs the reduction of gross to net performance only applies to climb. Runway data is not factored, other than the all engine takeoff distance.
Too many ground school instructors leave too many students grossly overconfident in takeoff performance data. If one is heavy for the runway available (or your company performance system “optimizes” data to get the lowest possible engine thrust setting), a few minutes of serious thought is warranted before takeoff. And there may not be comforting answers to some of the questions.
It is possible that the crew in this accident did everything right, just as the NW crew that overran 32 in ANC had done everything right.