After some digging, I think we have at least a partial answer. First, what I meant above was that probe sets are normalized independently, not that probes are. Each probe set contains multiple probes that go into the single intensity value. Some genes have multiple probe sets, which are (and should be!) treated as independent values. This post discusses which probe set to choose per gene.
As for the z-score, these appear to be calculated separately for each donor. You can see this by looking at gene expression for XIST , which is on the X-chromsome and dramatically higher in females than males. You can see that all donors have both negative and positive Z score values, even though the log2 expression in the female donor is much higher. My suggestion would be to try recalculating Z scores from your b or c separately by donor to see if that reproduces the results of a and d. These analyses were all done more than a decade ago and many of the people who worked on this project have left the Allen Institute, so thank you for your patience in sorting this out!