Well, first he said 'no'.
No, Atom is completely different from a Core2.
Then he said 'yes'.
Core2 instruction set with tune=generic is still the best to set.
Then he said (paraphrasing) 'I'm clueless'.
Anyway, a quick Google search turned up this spec page
on the Atom.
Notice that there are several models; only one is dual-core, and two are 64-bit. I would think you need to match the bit-rate, instruction set, etc for it to work properly and gain the full potential of the system, so it really depends on which Atom you have.