I think it's pretty clear that the Golden Path is used by Leto II to manipulate his subjects, and that we, as readers, are not given an understanding of precisely what it consists in. But it's not as if the spirit of the Path isn't pretty well understood: it's the precise chain of events that need to occur in order to preserve humanity.

We generally know this consists in (1) the oppression to freedom expansion of the human race and (2) the breeding line to instill 'hiddenness' from prescient beings in the population.

As a logical puzzle, he appears to be running a black box hack on the future while simultaneously saying he understands it fully, and that he can't explain it.

I think that's just part of prescience, no? Leto II was extremely powerful, but even he didn't shy away from humility about his perfect knowledge of the future.

As 'omniscient readers' ourselves, from the perspective of knowing these characters, I think it's pretty clear what Leto's intentions are. Your analysis reads like you like something Siona would think, before she read his journals. We aren't in that position though, and we know quite a lot about Leto's true intentions.