Isn't the fabric wetting out the same way any other piece absorbs moisture?
One problem that may occur with puffy under shell is that you get a little sweaty under your shell, stop, put puffy on, puffy gets wet from the sweat you trapped under your shell.
This is why many alpinists do puffy over.
I find it's similarly useful for many spot & stalk situations. You hike to glassing point and sweat in steep country. Shell is on because it's windy. You stop to glass and toss puff over top for duration of glassing. Get up to move to next glassing spot and stuff puff in pack. At next glassing spot pull puffy back out. No layers change other than puff. For puffy under you have to move 2x as many jackets, triple annoying with a bino harness or blaze vest added to the mix.