The term "Modern Synthesis" refers to the concept of Modern Evolutionary Synthesis which describes the process by which organisms evolve. It may be interesting to approach the analysis of the album as purely evolutionary. We know that Versus is about war ("It's about wars between inter-dimensional gods" - Sparkles*, Yogscast 2015 livestreams), and there are references to evolution ("We adapt, mutilate, replicate and survive").
We can therefore perhaps reason that Modern Synthesis refers to the evolution of war itself. "The Contract" being the situation that two parties got themselves into conflict in the first place. "Watchmaker" being about a 3rd party ("middle child of eternity") who needs resolution of the conflict. And "Versus" being the climax of the war itself ("This is the volta, scuttle the ships there's no return"), the volta being the turning point, the point at which reason and negotiation breaks down and the war begins. We may also consider the artwork of Versus to show a conflict (two factions split and tearing apart"), with the "middle child" stuck in the middle of them.
If we wish to link this to Cassandra, we may infer that the album beginning with part of Override is yet another reset of Cassandra, and the timeline has been reset to try and acheive a different outcome.
But of course until the album is released I can't really make assumptions... ^^
(god damn I missed analysing lyrics like this)