It's a common house rule (that I disagree with, but hey).
Note that certain spells or weapons have this effect : there's a magic arrow in the Book of Vile Darkness that passes straight through any evil creature, and therefore the firer can ignore any evil creatures in melee with his target for purposes of determining whether he incurs the -4 penalty.
I can't remember if it was a rule (FAQ, Sage reply?) or someone's house rule suggestion that the RTA for a Disrupt Undead spell ignores non-undead creatures in melee with the target as well.
-Hyp.