As far as I can tell, the Gradient Map takes the foreground color and background color, forms a smooth gradient, and maps it to the brightness levels of the image. While black and white works well, I have fun with complementary colors. You can play with the brightness and saturation of the colors you select for foreground and background.
I suppose the reason your relatively flat-looking scans become more contrasty is that the lowest value of your image gets mapped to 0,0,0, and the highest, to 255, 255, 255. Try scanning at even lower contrast, and use the Info panel to find the brightest and darkest values. Then do the same after applying the Gradient Map.
You can control the ultimate range of levels by using the color picker to limit the white to less than 255 and/or limit the black as well.