Manual mode is great, but it won't always compensate well in place of HDR. HDR works by taking several shots at once at different exposure settings, then combines them all into one image. In manual mode, you only get one shot. If it's a scene with both bright and dark areas, you're going to have some sort of tradeoff. Either one area too bright one too dark, or somewhere in between that results in neither being exposed all that well.
If it had a bracketing function in manual mode, then you could do HDR shots that way with some advanced manual editing. Since it doesn't, you're better off in auto mode with it turned on.