Well I'll be interested to read what others have to say.
I think it depends upon the recipe writer. Sometimes there really doesn't seem to be a good reason and I omit one or the other flavoring. But on the other-hand I can see how using it in combination with typical extracts from the grocery store (which aren't as natural as brands professionals typically prefer) might help tame the over kill of the extract.
But then I'd also agree with Suzanne that it does enhance flavorings.
Vanilla is a flavoring that is compatible with many sweet flavors, but it doesn't work with everything. A lot of tart fruit flavors are often enhanced by vanilla, such as fresh pineapple or apple. But into an almond cookie, it would be a wash. The real flavor I'm looking for there is almond, and I don't see the point in adding another flavor. It would compete; and really, you'd have to add so much vanilla to even detect it over the almond.
It reminds me, in a way, of painting. A lot of artists have used underpaintings to bring out a mood in a painting. Titian used to use red to create warmth under the skin of his figures, and it really brought them to life, without us really noticing how. I think of vanilla the same way. It should be there without us really noticing it.