If you need that silicon to actually work, then it's not free. Floor-sweeping is necessary because the more stuff you put on a chip, the more likely it is to have defects. That really is an extra cost. I don't think there is any way around that.
But I think you are overestimating how low-end these chips are. See http://arstechnica.com/gadgets/news/2008/02/small-wonder-ins... for example, which shows that the Silverthorne architecture (1st Gen Atom) has pretty much the same transistor count as a Pentium 4.
No one thought that the fact the Pentium 4 had to support x86 was a significant factor vs other architectures. For the chips we are talking about, the cache memory takes more transistors, so the quality thing is pretty insignificant too.
The situation is even worse for graphics cards