That's a very good X-Ray machine!
Email from an X-Ray Tomography Specialist:
"The reason you can't see the copper traces is because they are planar to
you / perpendicular to the beam. Xray detectors have somewhat limited
contrast, and in order to get good penetration, you need to run high kV
to get good energy (material penetration), and have decent current
(flux) in order to have enough signal on your panel. If you have hard
enough beam (good penetration) to get through that steel you will
absolutely blow through thin pcb traces. When the full thickness of
those vias is exposed to the beam, the beam has to pass through the
equivalent of that thickness of copper, hence you can see it."
That's only half true.
The X-Ray is like any other electromagnetic wave.
The energy (in kV) sets the wavelength of the X-Ray light - so a bigger energy penetrates denser materials easily, the power (in A) sets the flux, so more power is the same as more light in a standard illuminator. At the shown energy levels (more than 100kV), most metals are semi-transparent, so the X-Ray light simply pass through the copper as light passe through glass.
Now, imagine the PCB made from glass, the vias would be visible because the light *reflects* on the vias if the light angle is low enough - the same is shown here with the X-Ray. Also, if there is some lead in the vias, lead is much more denser than copper, so it also will be a lot darker in the X-Ray image.
Most industrial X-Ray machines also have filters in the X-Ray generator to filter out the low energy light - the most used filter is simply a copper sheet, this will absorb the low-energy light and produce a much better X-Ray beam. You normally can change the filter to select different X-Ray wavelengths easily. I suspect that to actually see the traces you should select about 70kV energy and remove the filters, then the copper will be much less transparent than the other PCB materials.