As long as the league creator has the option to schedule the frenzy anytime, including at the same time the league fills if it was so desired, then I don't see the problem. Would it be difficult to include an option of "immediately after draft runs" to go along with all possible time slots?
Also, it could be difficult to predict when a league will fill. What if someone sets for the frenzy to begin at 3:00 PM and the league doesn't fill until after that, like 4:30 PM for example. That will throw everything off.
Of course I've never done a frenzy before, so I could be missing the point entirely.