Eb said he saw the man, not the soul. And I'm not saying he "definitely" didn't gaze him, I'm saying he definitely didn't say "Gazed."
His exact line is:
"She met your father. A man. A mortal, without powers, without influence, without resources. But a man with a good soul, like few I have ever seen."
He is explicitly commenting on the quality of his
soul, and comparing it to other souls he's
seen. That strongly implies that he saw Malcolm's soul, too.