One of the joys of writing a new version from scratch is the ability to improve and re-think many of the small imperfections from the previous version. You'll find that v2 is full of clever little touches that will make your experience more pleasant.
Andrew took great pleasure in improving this particular aspect of the user experience; Users with external screens would occasionally find that Alfred was confused about where to appear on screen after disconnecting from the second screen. The preferences for v2 resolve that, as you can position Alfred's window on your screen and, regardless of your resolution, he'll remember it next time.
This is one of the many areas that have received attention and polish to make using Alfred as pleasant and easy as possible. You can look forward to discovering the rest for yourself during the beta!