From what I can gather, it seems FlexyCore generates more efficient, architecture specific assembly code at build time. This is where the performance gains come from.
A little deeper reading shows that it does this through the Dalvik VM, the VM on all Android devices.
A little deeper reading shows that it does this through the Dalvik VM, the VM on all Android devices.
I think the creator can say it better than me: http://www.youtube.com/watch?v=tEAz9fRoDmA