Self-explanatory; I often find myself making tiny adjustments to positions using the manipulate window, and if I try to undo an action I’ll often have to wait several seconds for it to clear away before I can continue, with two undos completely obscuring the window.
They could be moved to the top-middle, just below the inventory, or they could just be displayed beneath the Manipulate window. Maybe even add an option to disable the popup in the Game/HUD settings?