I believe that the purpose of Stardates is to provide some sort of compromise between many disparate calendar systems. There are supposedly 1,000 stardates per Earth year, but that's never been confirmed in-universe. It might just be approximate. For all we know, a standard Starfleet day might be an average of the day lengths on several different worlds. Just because they break it down to "hours" and "minutes" does not mean those words mean the same thing.
Either that, or the universal translator converts between calendars for everyone.