IIRC the calculation searches for results with the best gradient (the highest permissible tkof weight in disguise). So to overcome the drag penalty of F3, higher V2 is chosen - it suggests that it climbs better with higher speed.
Aero theory supports that. Max L/D for a given configuration is pretty constant but in order to achieve it higher speeds are needed for higher weights. Perhaps F2 does not drag that much and the markedly higher speeds are not needed. Yet second-guessing an iterative algorithm is rather pointless.