Yes... you can move it, but you'll have to edit the layout files to do it.
Edit [ Interface > AddOns > nUI > Layouts > Default > HUDLayouts > {hud mode} > nUI_HUDLayout_{hud mode}.lua ] -- near the top of the file is the layout section for the cooldown bar. The "message =" section is the one that defines where the alert message is printed and the "yOfs" option is the one that defines the vertical position of the text. You can use that to move the message up or down.
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