Hello Eladio
Please allow me to change your example sentences a bit for the sake of explanation.
[1] I would rather (
he tell her than I do).
[2] I would rather (
he told her than I did).
[3] I would rather (
he had told her than I had done).
As you know, "would rather" is equal "wish". Unlike "want" and "hope", "wish" and "would rather" are used to express the subject's desire that is counter-factual (in the case the desire is about a past event or a present event) or can hardly be realized (in the case the desire is about a future event). Because the desire is counter-factual or unrealizable in nature, the sub-clause for the statement of the desire is expressed in subjunctive mood to show its unreality.
#1 is about an unrealizable future event. "He tell her" is a subjunctive present.
#2 is about a counter-factual present event. "He told her" is a subjunctive past.
#3 is about a counter-factual past event. "He had told her" is a subjunctive past perfect.
paco