I would say that scene was scrapped because it missed that Touji, Hikari and Kensuke were out of Tokyo-3 in EoE (IIRC, aren’t they seeing fighter jets traveling overhead to NERV?). PS. By the way the Tv CM (professional) for the EoE film is pretty strange… No way I’ll allow you get rid of me" ("idiot" was eliminated in the storyboards… and the complete line was modified, sooner or later).