Microsoft is constantly tweaking the user interface in Windows 10 to make sure the experience is cohesive and that trend will continue with future builds of Windows 10. One area that will be updated in an upcoming build is how searching works inside the OS and the use of Cortana.
In the current builds, when you search, there is a pop-up window that overlays the desktop and the Start menu that results in the ugly experience that you see at the top of this post. Now that the new Start menu has been deployed to Windows 10 - this version of the menu is written in XAML whereas the previous Start menu in Windows 10 builds was written with Direct UI - search will be integrated into the menu rather than being a standalone feature.
According to our sources who have used the builds, searching will now be done inside the Start menu and do away with the overlay that currently exists in build 9926. This change makes the Start menu the functional area for searching and could be part of Cortana as well. Seeing as search is now inside the Start Window, it would makes sense that Cortana would migrate this way too.