All 3 are very similar. #3 is more formal and less common. I'd likely say He's probably not home right now.
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seagullCan we say (C) to mean about the same as (A) and (B)?Sure. (C) (may well) means "it's quite possible that". That's about the same as "probably".
seagulldoes (C) sound natural to native speakers?Not so much with the negative 'not'. The affirmative sounds more natural to me. He [may/might] well be at hom
seagullI just ran across an English question that requires test-takers to express this idea using a modal verb. I'll answer it, "He may well not be at home right now,"That's probably the best choice if you must use a modal verb.
CalifJim Or should I say "That may well be the best choice if you must use a modal verb"? CJYeah. I think we may well be confused when we must solve such a difficult question.