I like Silver's model better, and it explains the contradictions just as well. The contradictions arise in part from the groups with no overlap and a shared rhetoric. The Religious Right and Moderate-Reformists both say they want small gubmint, but that means completely different things to each of them. Nonetheless, at the end of the day they both get called Republicans.
Silver's inclusion of the Establishment is also very important to the model. Because the establishment has overlap with each of the four other factions, representing their foothold in controlling the greater party, it has the least "purist" members of any faction. This is not exactly surprising when one considers that to be a Pure Establishment Republican means being for each of the other four factions equally in the name of strengthening the GOP's institution. As before, there are not many informed people out there who could say they'd vote for members of all four other factions with equal enthusiasm, because several pairings would have little-to-no overlap.
As for the GOP Civil War, it is starting now with the breakdown of a critical link in the factions: the Libertarian-Tea Party overlap. As the Tea Party is driven more towards a state of frenzied far-right rhetoric, the Libertarians who originally allied with them in part are shying away (and thus by definition are moving closer to the Moderate-Reformers). With this link broken, the party is immediately divided into centrist-to-center-right (Libertarian-Reformer alliance) and right-to-far-right (Tea Party-Religious Right alliance) wings. The Establishment is stretched thin because what was previously a four-way fight with equilibrium has turned into a two-way tug of war between the two alliances. This will only further deplete the already small "Pure Establishment" as polarization increases. In the end, what we are seeing now is turning the GOP into two different parties with the same name, even more than they were before.