An overtone typically refers to an implicit meaning detected by "reading between the lines". For example, describing the consequences of certain actions in a perfectly neutral tone could still convey a threatening overtone.

An undertone typically refers to an implicit meaning conveyed by the manner of the utterance, that is, a literal sound in the voice that conveys the meaning. So words that are growled, hissed, or said "with an edge in the voice" carry an undertone such as anger, frustration, or sarcasm.