When in auto modes, the EV compensation dial will choose various combinations of aperture and shutter speed and ISO to increase or decrease the exposure. When in manual mode as you suggest, the only variable left for the EV dial to control exposure is the ISO. So in that case they are virtually doing the same thing, but only in that particular situation. If in aperture or shutter priority or fully auto modes, that exposure compensation dial will control more variables than just ISO.
Also, I believe that in this case you describe, the EV dial will only have an effect if it's set to Auto ISO. If it's set on a particular ISO value putting you in FULLY manual mode, the EV dial will not do anything.
