I didn’t realize this thread was as recent as it is, but I’ll go ahead and apologize for resurrecting it anyway.
The reason I’m doing so, though, is because I have not only an answer but the answer, obtained directly from Brad Dourif himself this past weekend at Dragon*Con. I asked him about the gestures, and I asked him which side of the camera the idea came from.
It’s acting, and it was all him.
He said that playing De Vries was a challenge, specifically as to finding a way to present the character’s massive intellect so that it comes across on screen. He decided that the way he would do it would be to show the character speaking two languages, one verbal and one gestural.
He also claimed to have suggested that Lynch go ahead and film the sequel to Dune while they had all the people and all the sets and everything ready to go, but in spite of this, I think he’s a pretty good guy. 