Sometimes this is done for weathering purposes. They will paint a base coat of silver and then the exterior color and then chip and flake the outer layer of paint off to get a 'weathered' effect.
I think this is probably more common in automotive modelling, though. (Someone correct me if I'm wrong) Since a lot of automotive colors are semi-transparent or even transparent, the color of the basecoat will, a lot of times, have a major effect on the final color of the paint. I haven't done a lot of experimenting myself but with all the 'Kandy' colors and other semi-translucent colors out there, you can get an enormous variety of tints and hues of one color of paint simply by varying the color of the basecoat.
Hope that helps you out and I'm sure there are others out there that can explain it better than I can.
Ray