A-FLOOR The configuration anomaly at NBO (D-ABYB) was further compounded upon leaving ground effect due to higher density altitude/high elevation airport. (5300+ feet).
If Vr appears to be long in coming and if the end is near, an unwritten technique of last resort would be to immediately "firewall" the throttles and extend flaps another notch...just to get off the pavement intact. But if leading edge flaps had stayed retracted at YHZ, as you had theorized in one scenario, then this desperate last minute survival measure would have made no difference either.
