Simple GIGO. The EK procedure is designed to try and trap the errors via Gross Error Checks and a final cross check of the lap top Green Dot, Minimum Clean speed and the Minimum Clean Speed in the FMS.
At 360 tons GD would have been about 265 ish, at 260 tons 30 kts or so less. If they had followed the mandated procedure they would have caught the error. However even if they hadn't followed the procedure I would hope most pilots would have the awareness to recognise that a 360 ton A345 needs Flap 3 not Flap 1, 170kts ish to rotate and 265 kts for minimum clean with a flex somewhere in the 30s not 74. That a crew did not know that is a concern and the lack of awareness maybe points to a complacent rather than questioning culture. Also reading the report I wonder how many of us would have selected TOGA having reached the 900m to go markers without any obvious signs of getting airborne.
Earlier someone questioned the level of thrust reduction. The max reduction from Flex is around 25% depending on the airport so they would have had probably 20% less thrust than expected during the take off roll.
Some may think I am harsh but I feel sorry for the guys on a personal level but not professionally.