News Researchers Can Now Reverse Engineer Entire Chips With X-Ray Technology

This is not so simple. After getting the complete transistor + interconnect layout, you would need some kind of synthesis tool in order to guess (interpret) what part of chip serves what high-level function.
 
Hmmm, maybe shielding the internals of the chip with a layer of Pb would be a good countermeasure
Some chips are allegedly bonded to their heatspreader with solder. However, I don't know if that ever contains lead, or how much lead you'd actually need to effectively block these x-rays.

I wonder if this can be used for troubleshooting, or to measure things like metal migration.