You can close takeoff windows down during takeoff (see left). Traditionally clicking the X in the top right corner with your left click button will close the window down or right clicking with your mouse on any blank part of the window will also close that window down. In this example an assembly list is being closed.
The image on the right shows that you need to do the same for any additional takeoff windows you may have open. In this example a catalog is also being closed.
Left click your mouse in any open space in the sidebar menu will close all takeoff windows simultaneously.