The biggest flaw with the sequels is that they end up not ending- in the same way the Dune Messiah was a setup for Children of Dune, it seems that Heretics and Chapterhouse were leading up to the seventh book that Herbert died before writing.
While their writing is not as brilliant as Frank Herbert's, the books they wrote, mainly the prequels, have helped me understand just how big the original vision was and have helped me enjoy the sequels more. God Emperor is truly as masterpiece, but it took a couple of reads, and the sequels, for me to appreciate it more.
The prequels are basically Star Wars books set in the Dune universe.
The same way KJA "improved" Star Wars.
His wife, incidentally the editor-in-chief of the publishing imprint that then owned the publishing rights to the Star Wars and Dune literary universes, is to blame for unleashing his word vomit on mankind.
(I personally do believe that some notes were left, but I suspect they were not complete, and were utterly ignored by Brian & Kevin. Because they is no explanation which makes more sense. There's no way he would have tied up with series by referencing characters never-before introduced from before the previous books.)
So, maybe? I lean towards thinking there were notes myself, as I can't see anyone making up that ending de-novo.
It seemed to me that the two figures in Duncans visions were going to become important, but they'd be rogue/evolved/advanced face-dancers rather than representatives of the machine intelligence.
I guess we'll never know for sure unless the notes are published.
Given the lengths that Frank Herbert went to avoid having computers in Dune, it would not make sense for his big bad to be a computer revealed in the last few pages of the series, especially when his big bad was always intended to be Destiny.