It does make sense. Introduced from the very start as an astoundingly dumbed down and volatile take on the character the New-52 Superman was often contradictory and schizophrenic in presentation - at turns admirably self-sacrificing and adamant on helping the helpless, and on others a damaged aloof outcast who was either moodily distant or unforgivably violent. With some particular writers holding him as every bit as heroic and wondrous as he ever was in the past, too many others pushed forward with the bitterest aspects of the New-52 ethos and determinedly ground down Superman's potency and self-belief to the point where he was the least 'Super man' of them all... his lot was too often a constant struggle, not just within himself, but with the demands of a role he seemed fundamentally ill-equipped to deal with. Few could argue that after five years of exposure to that treatment the contrast between he and the returning Superman seen in Convergence and Lois & Clark was very nearly the difference between night and day... an old close and dear friend had come back to save the day. And in more ways than the one.
A godlike being who can restructure reality and targets Superman for elimination is nothing at all new to the Superman mythos, and in every such tale those beings have been seen to be still limited by the clay they are working with and, in the end, their own unadmitted self-limitations.
It is perfectly possible for a Doctor Manhattan or Time Trapper to kill Superman outright, in principle at least, in practice though the deed is not without its repercussions and for a scientist like Manhattan it is the experiment at hand that concerns him, whether his taking advantage of the Flashpoint effect was chance or planned it does appear that he saw the opportunity as a means to conduct a sociological examination and reduce the Earth to a more bleak fearful place to live in and see what course it took. To make this experiment work he had to proportionately diminish the power and potency of the superhuman hero population by deleting a decade from their natural growth and at the same time ensuring that the likes of Superman and Wonder Woman failed to rise to the status where they could, by strength of their own personality and example, act as figureheads and icons for the fearful masses... in a peculiar way the as yet unseen Manhattan Is acting out the same mandate and philosophy as Darkseid himself.
But the notion that Superman is an integral part of the universes structure and a nexus point to the meta-textual is not at all a new development. That the meta-physical Doctor Manhattan might respect and be wary of his place in the scheme of things is perfectly in line with what we have seen of previous such problems - the Mandrakk's, the Dominus', and Vyndktvx's have all faced the same dilemma as this, and all have had to face up to the reality of their own limitations in regards to this... it isn't a question of power, so much a war of philosophies and ideas. Superman is the physical and meta-physical embodiment of one set of universal principles, the likes of Doctor Manhattan and Dominus are representatives of the other. And this then is what we are seeing being played out with the Rebirth mission and its ultimate destination in whatever it is that Geoff Johns is charged with developing...
Why not have Superman is sorta like how Marvel view Adam Warlock for a time, as the godslayer, who represented life and light, and not even the more powerful Thanos, his counterpart, could really slay/stop him!
Superman maybe has a direct link into the presense or some other powerful entity in the DCU, maybe even Mxy in a weird way as his back?