This is speculation but I think there may sometimes have been a holed stone stood up in front of a barrow that was a symbolic portal. The hole was too small for an adult to negotiate - in one piece. Worse, I believe some of the pierced stones had rectilinear holes. (There's a barrow in Smithills that demonstrates this association - http://www.themodernantiquarian.com/post/34768 - and the perforated stone is incorporated into the wall in front).