Somewhat related to: Should the rep recalc award accepted answer and bounty points at the end of the day
While bounties themselves allow you to go over the daily rep limit, they will still affect your limit in that if you receive a 200 point bounty at the beginning of the day, you are barred from getting any more rep (other than accepted answers and more bounties) that day.
Therefore I would like to suggest that regardless of the time of the day in which a bounty was started, the end of that bounty should always be the end of the day (before server time rolls over to a new "rep cycle").
Edit: Case in point. I just got awarded (approximately 8:30pm EST, a half hour after server time rollover) a 250 point bounty and I am already over the rep limit. I don't think this is good at all for users and it almost seems like a disincentive to continue posting questions and answers.