The AKL incident (or accident) was a repeat of a similar SQ incident about a year earlier, in which the crew climbed out at V2 - 8kts. Both were caused by the fleet's procedure of overwriting the FMC computed figures with data from the airport analysis tables WITHOUT the requirement to check any differences with the FMC figures. It was a classic case of history repeating itself. Maybe the EK report will compare with the earlier T/O incident at JNB.
The problem may be in the method used to determine T/O performance figures rather than measures used to check the accuracy of those figures.
Personally, after "re-learning" how to obtain the numbers the SQ way, I wrote a list of V2's and EPRs for every 10 tonnes weight on the back of my clipboard and would set the V2 according to the flight planned T/O weight on the MCP during pre-flight scan checks - it gave me an instant cross-check when the co-pilot produced the figures for T/O from the loadsheet.
Methods for determining thrust/speeds vary from airline to airline for the same a/c type, few airlines seem to train such extractions well.
I would generally agree about the presence of both augmented pilots in the cockpit before departure - one is a useful extra pair of eyes, two are usually a distraction ( too much superfluous chat!).