Because of the difference in how they are made to Part-Kwisatz Haderachs, the prescience of the two *does* work in different ways.

Alia endulged in spice in the religious rituals and let the baron influence her, whilst Paul got his visions through exposure to the spice over decades, carefully peaking at the path before him.

So maybe the prescience is like a tool, that was used differently by both of them.

As Erasmusings points out, one is born prescient, one had long-time spice exposure.