Have you heard of a scintillator? They are much more efficient than a GM tube and can be constructed from various materials. You can construct them out of silicon, but the energy resolution is poor and does not allow for isotope identification. Using a NaI(Ti) crystal would have allowed them to both measure absorbed dose as well as identify the types of radioactive materials present. As there are commercial products today which are the size of an iPod and detect radiation, I see this as a feasible product.

You would want the tight integration if you wanted to steganographically store the recorded information for covert exfiltration. The agencies driving this have a high level of paranoia and may have deemed this necessary for a variety of reasons.

There are other detectors you could use. You can use a simple photodiode too. But generally they don’t have the same sensitivity. Generally the sensitivity is too low for most radiation monitoring applications as I understand it.

Steganographic storage would make sense, but the article mentions storing on a separate partition.

So the tight integration still seems odd to me. Another comment suggested that they wanted to gain general “iPod” modification skills for other projects. That seems like an interesting idea.

As an aside... I kind of like the idea of playing specific songs, or a sequence of songs to trigger a secondary processor (which is sampling frequencies played). This could potentially take over the USB port if necessary.

That generation of iPods used hard drives, it was possible to replace those with smaller flash drives. This would give you a lot of space to add sensors/secondary compute. And could be done without coordinating with Apple.

It does seem weird that they took the chance of this leaking too... and I would have thought they would have taken any other route possible.

This is DoE I think, not any other 3 letter agency, so they're probably not too worried about it getting out after the fact. Who the hell uses an iPod anymore? Now you'd just use the CCD camera on any modern smartphone, or count DRAM bit errors or something. Then again, they could have done that with the iPod and didn't, which suggests they wanted to measure energy levels maybe. Tight integration makes a lot of sense if you want something that, when opened up and compared to an off the shelf iPod, doesn't look any different.

CCD cameras or counting bit errors doesn’t really have great sensitivity for radiation detection. This is why they are generally not used to monitoring projects and people stick with Geiger tubes. This is my understand anyway (having worked on these kinds of projects).