Using full length does not necessarily mean more runway left at rotation, quite often it just means more use of de-rated thrust or a delayed v2 climb profile and you rotate roughly same place anyway..
Indeed , an anecdote : The first time I jumpseated on a A380 ( out of FRA taking off on 18 ( 4000 m ) I was extremely surprised and even a bit worried at first to see that the take off roll was started with only the 2 inner engines, and only when passing 60 Kts were the 2 outer engines throttles moved fully forward , then a rotation almost at the extreme end of the runway I was explained later it was a flex take off and due to the very long runway available, they only needed to add power on the outers at 60 Kts , to avoid possible FOD ingestion on the outers which were hanging over the runway edges,
They could easily have taken off with much less runway ( we only needed 2800m at our T/O weight on that flight) . Difficult to make a judgement if you are not the PIC of a particular flight and do not know the numbers.
Anyway this accident here is not an intersection accident , it is a take off distance/weight miscalculation one , a bit similar to the 2003 Singapore airlines 747 that attempted to take off with a TOW error of 100 tons. ( and a 330 in Australia that did the very same a few years later) so all human errors as you correctly mention. and not procedural ones.