When he went back and observed Jon and Janey at the Carnival; and altered their realities. Were they all transported to that reality? Or did reality seem to just bend to his will.
Think pre-retconned Beyonder. You can't just wave all his feats off as BFR.
You don't like the nature of his reality warping because it's not poof, magic!
It's based on a scientific experiment in which physicists shot a laser beam through two slits expecting to see two slit-shaped lights behind it. Instead they saw hundreds of lights. The particles that made up the laser were in several places simultaneously. They tried observing the particles individually and then fired one beam through two open lines in the wall, and this time,after passing through, there were only two lines of light. Somehow, by virtue of watching each and every subatomic particle, they controlled the particles to have one definite location in temporal space.
It's called the measurement problem.
Doctor Manhattan applies this to everything that exists. He manipulates reality because there are infinite realities (Many Worlds Theorem), he just needs to pick one and its in front of him all the sudden. It's not BFR.