If you're not planning on using a pico and if you're not planning to use several 3.5'' drives, your best bet for power consumption is the Intel board which takes DC. Not using a conventional power supply is going to make a much larger difference than undervolting.
Just wondering if I could get close to Atom power consumption (but with better performance) for the latter phase.
No (not even close) because there's no such thing as "Atom power consumption". If you pick an Atom board for its power consumption and not for its features or price, it'll destroy the competition.
Undervolting doesn't make a big difference when it comes to idle power consumption anyway.
You're better off buying an Atom board especially for the "latter phase" if you want lower power consumption. The resale value of your Sandy Bridge mobo + CPU might be higher than the cost of the most efficient Atom boards anyway.
the Intel board uses less power in stock config
We don't know that actually. It's possible but have you seen any evidence?
Intel's boards tend to have better power consumption than the ones sold by gamer darlings but Biostar is one of the vendors which has been known to sell efficient boards.