stating openly what the theme is intended to be (which may or may not actually carry through into Doomsday Clock, as Rebirth #1 was written well before Johns had an actual story idea for the Watchmen crossover) doesn't mean it actually aligns with the text of Watchmen, the DCU under Johns, or the character of Dr. Manhattan in the original story.
Not sure I'm following you here. In comparison to the DC Universe, the Watchmen universe is certainly an inherently more cynical fictional universe, both within the perematers of the universe itself and on a thematic, meta-textual level. Just look at how Ozymandias "saved the day" at the end of that book by engineering the mass-murder of millions of people to unite humanity by fear. Of course, and as people often have a tendency to forget, there are definitely elements of hope and optimism to the story too (Manhattan's epiphany on the sanctity and miraculousness of human life, Laurie and Dan's genuinely tender burgeoning relationship), but as a whole...I would argue Watchmen is very much a treatise on why comic book heroism just wouldn't work in the real world, and how real life "superheroes" would only be driven to do the things they do on account of crippling psychological hang-ups (Rorshach), or a deep-rooted desire to inflict violence on other human beings (The Comedian). Doctor Manhattan himself is an intensely nihilistic, emotionally disengaged individual who even despite his revelation on Mars, embodies a lot of the core themes that Watchmen represents. For the most part, there's a pervasive, deconstructionist tone of Watchmen, which at its basest level is very easy to contrast with the much more lively, hopeful and adventurous tone of the DC Universe by its very nature as an emphatically superhero driven world. In terms of "aligning with the text of Watchmen" or "Doctor Manhattan", on some level, all Rebirth seems to have wanted to achieve, both based on the text already laid out for us in the comics and emphasized by the writers themselves, is utilizing the clash of tones and ideologies of those two universes as fuel for telling a new kind of story. So criticizing the writers involved for not seeming to understand the irony of combining an "anti-superhero comic" and a "superhero comic" doesn't only seem to miss the point...it's basically making the very point the writers seem to be making themselves.
I don't know. The jury is still out, obviously. We need to see how the story plays out to its conclusion before we can get too much in whether this particular story worked or not at a thematic or narrative level. But at the very least, from what we've seen, there seems to be enough self-awareness in what they're doing to maybe garner some confidence in the story that they're trying to tell. Maybe.
Apologies if I misinterpreted the point you were making, incidentally. If so, feel totally free to dismiss my reply.