Well, that is because he is from outside the metaverse. The problem with Manhattan was than he could se his world already happening, immutable, without any change. But in the DC universe, he was aware of the changes happening but meanwhile he was inside the universe. Any other characters aware of the changes than transpired in the DC universe either were outside of the proper universe/multivere/metaverse or he/she learned about the changes after they happened, by other sources.
That quality of being a timeline more flexible is what allowed to Manhattan change history. This new universe already had the quality of change. Manhattan only exploited a trait already present.