Am I right?

He came home by six o`clock OR He had come home by six o`clock.

Both sentences are written correctly.  However, they have different meanings.

The first sentence using the simple past tense simply expresses a fact:  He arrived home at or before six o'clock.

The second sentence using the past perfect tense indicates that John arrived home before something else happened.  Here are two events:  (1) John arrived home by 6:00, (2)  I arrived there at 6:30.  Here's a sentence using the past perfect tense to describe that:  "John was already there when I arrived at his home at 6:30, because he had come home by 6:00."

In your example, you did not tell us what happened before "He" arrived home.  But if we had a fuller context, we would know what it was.  Example:  A:  "Was John home when you arrived at his house at 6:30?"  B:  "Yes.  He had come home by 6:00."