Well for one unlike Atom, the MV-40 is a regular x86 CPU thats just low power by them ripping out a lot of extras that make the desktop version faster like a slower HTT link, lower clock speed,less cache ect.
But the MV-40 runs on 3x the thermal limits of a normal Atom. A normal Atom runs at 5w TDP. The MV-40 is set for 15w. I think that the dual core Atom hits 10w so a dual core version of the MV-40 would be 30w.
So in essence, the MV-40 is great if you want more performance but if you want battery life on the go a Atom will trounce it especially since Atom will be using a low power Intel IGP while the MV-40 will probably have a higher TDP ATI GPU.