How do I optimally cut a bolt to length?
After cutting the bolt to length, use a stationary grinder instead of a file to clean up your work. With a grinder, it's easy to square up the end of the bolt and apply the chamfer that you want.

Just be careful, especially if the bolt is shorter than the grinder's table. If the bolt is short, use a pair of vice grips to hold the bolt during grinding. And remember that the end of the bolt is going to be very hot after grinding!