I really doubt that it makes much of a difference. The scenario seems overly hypothetical since applications are never solely numbers on a paper fed through a mathematical formula. HBS is looking for a certain type of individual - people who have a habit of leadership, not a checklist of accomplishments. This is important to adcoms because there is a much higher percentage of applicants capable of completing the MBA coursework than there are seats available, so adcoms try to predict future success more so than whether one can graduate. Having a Harvard master's probably means very little to admissions, especially if the master's degree was easier to get into (for example, a lot of people are admitted into the Kennedy school for an MPP/MPA but get rejected from HBS).
Harvard undergrad might be different, though. A high percentage of HBS did go to Harvard College.
FWIW, I know someone who is currently earning a master's at Harvard, applied to the MBA program in September, and just got rejected. Yes, this is an N of 1, but I don't think that that is unusual, either.
///EDIT/// That said, if you really want to apply, then apply, and don't worry about the odds. If it's your dream school then don't reject yourself because you'd always wonder.