Why would pumpkin pie form a clear custard layer?
I believe that your aunt is right and Grandma added cornstarch. Quite a few times in the past when I've made sauces using cornstarch in a saucepan, bubbles of clear gel have formed when I've neglected to stir constantly. It seems quite possible to me that a thin layer of this gel would form when making a pie, rather than the bubbles that I have seen.

I understand that you want to come as close to Grandma's recipe as possible and keep this layer. Bearing in mind that I've not tried this, I would mix 1 to 2 tablespoons of cornstarch with just enough milk to make a pourable, non-lumpy paste and whisk it gently into the custard  . If the recipe involves any heating of the custard before baking, be sure to incorporate the cornstarch mixture only after heating.