While re-reading the whole original series, I noticed that at the end of God Emperor and repeatedly through Heretics, Frank Herbert speaks of multiple universes.
No Ixian machine can do what we, the descendants of Duncan Idaho and Siona, have done. How many universes have we populated? None can guess. No one person will ever know.
The no-ships had, indeed, seeded those other universes with rot.
... might provide meat for some of the most expensive meals in their universe ...
I have always thought of Dune to play within a single universe. I think this is also necessary for prescience to make sense in the way it is described. Multiple possible futures of the same universe are seen and can be tried to reach or avoid by decisions in the present. Things would always collapse onto a single timeline. As far as I can tell, there was never any mention of a multiverse with parallel timelines caused by any decisions of Paul or Leto II.
Does the author just use "universes" as a substitute for "galaxies"? Or, more generally, bubbles of humanity isolated from each other through the scattering?