I think the good doctor is being underestimated here
No, he's being overestimated. Dr. Manhattan cannot hang with the vast majority of powerful characters in other comic book universes. He lacks the concrete feats to actually contend.
even when he is busy vaporizing opponents
And who has he destroyed? Normal humans? A tank? Meanwhile, people like Strange and Thor were out fighting cosmic beings on a galactic scale. Manhattan can act tough by fighting humans as much as he likes, but he's never had to fight somebody as powerful as Thor or Strange. He doesn't have to feats to suggest he can resist energy / molecule manipulators, nor has he shown sufficient ability to harm people like Thor or Strange, who actually have fought beings with energy / molecular manipulation.
Manhattan is big where he comes from. He is incredibly tiny in the Marvel U.
telekinesis, matter manipulation at atomic level, enhanced size... ok he might not have feats but those powers sound like some of the big wigs in the marvel universe to me