I suspect the performance calculations on the EFB were correctly completed; that the crew assumed the Boeing OPT would provide sufficient margins; and that the rotation was slightly after Vr was called. Swiss cheese.
Using the 'optimum' setting on that programme minimises pilot input/consideration of actual physical margins to the screen height, whereas the landing calculations always provide physical distances that one can compare with the available distance to the preferred exit or runway stop end.
On a lighter note, the video reminds me of base training, where every take off was a bum clenching 'experience'.