I'd disagree with the notion of Raven's current timeline being a mess, there are gaps in it, but as it is now we are pretty much poised to have another of the old TT vs Big T stories.
But hey, if you want to use the Trigon story to do some fixing, go ahead, since Trigon should be one of the few beings that would know about Manhattan, and possibly just used him to further his own goals.
... Actually, thats just another reason to save the story and build up to it. Imagine if you had the story and during it, Trigon lets slip he exploited what Manhattan did to get control over Raven and the story ends with Raven (and maybe others) gaining the same insight into what they all used to be. Or save him a bit longer and just have him take on Manhattan directly for w/e reason... like Constantine sent him on a collision course with the Mxy-backed Regime in Injustice.