it's not that they must save separately against each effect, but that the damage stacks. if the have damage reduction x/peircing, or whatever, that only applies once (if the second lightning bolt emerges from that spot). same with lightning resistance. any effect which applies when he is hit applies once! and then any additional bolts he might be in the area of apply normally. that is what is so unigue.
Edit: here is a quote from the same spell description "Fire resistance applies to each sphere’s damage individually" what I am saying is that, if you hit a target with the spear, and then branch another lightning bolt from that point (the square that the opponent is in) that resistance will apply once (unless you have more than one bolt branching from that point, in which the third and fourth bolts are counting seperately). in essence, it becomes a 12d6 attack instead of 2 6d6 attacks. you really shouldn't link to a site which directly contradicts the point you are trying to make.