Comment by Amezarak

The Siona gene didn't actually remove prescience, it hid people from prescience. That's why Leto II is still able to control events as far in the future as Chapterhouse Dune.

This is an important distinction. It's also the case that Leto needed the Ixians for the no-ship technology, which he also regarded as of extreme importance for the same reason. Which also, remember, the Idaho gholas had to be confined to no-ships so they, lacking the Siona gene, wouldn't be visible to prescience.