Goku loses but pre Crisis Superman and any Superman above rapes. Superman 1 Million is one of the strongest characters in DC and Mr. Manhattan is probably in the top 30.
That alone should tell you how strong the strongest version of Superman is.
Also, do you include SSJG Goku(even though it isn't his own power since he needs the help of 5 others to perform the ability, and not like it would really matter?)
why not?
one touch and superman can have him millions of years in the past.
being able to see your future is meaningless without the physical speed to keep up.
also manhattans personality is that even though he does see the future, he doesnt beleive in altering it.
he wont see a punch and think "man i need to dodge that one".
superman has resisted transmutation and atomisation before.
hell one of his opponents (darkseid) is ALL ABOUT beams that try to atomise people and supermans survived him.
you think he hasnt fought teleporters? again darkseid's all about teleportation.
you think he hasnt fought intangibles and energy beings? think again.
we got manhattan whos barely done anything except atomise street levelers and survive being disassembled vs superman who has 70 years of accumulated feats and combat ability. and who has undoubtedly battled gods who make manhattan look like a lightweight
no he cant.
we dont know the upper limits of his atom control. all we know is he can tramsmutate things and atomise humans.
it stands to reason that the many ki blasts and shit goku faces can atomise/vaporise matter too but he tanks those.
it also stands to reason gokus too fast and manhattan cant get a lock on him