It's just the way genetics line up... every once in a while you get a quirk... the quirk of being extra large is something that would help the fish survive, where many/most other quirks would inhibit them from thriving (deformities would be an example of one of these quirks).
Plus, people here are saying 5" is a "max size" for Mollies... so it seems your's isn't unnaturally huge, just growing at an unnatural pace. In time it may prove to be both though...
The more I've looked into genetics the more I've learned they are well over my head... It's one of those "the smarter I get the stupider I feel" kind of things...