The specification should say what happens with elementFromPoint in CSS regions. See mailing list thread.
I will take a shot at region API proposal for this.
Dup of https://www.w3.org/Bugs/Public/show_bug.cgi?id=21132
Whatever the solution for events turns out to be, it should also apply to elementFromPoint.
*** This bug has been marked as a duplicate of bug 21132 ***