This is the main reason why by default the device disables the RF source, you have to go out of your way to enable it by editing an /etc .conf file - however it actually does make a slightly better random stream
With the assumption that it only receives, I would strongly prefer that it be left on by default. Adding a second source to the CRC mixing can only improve entropy, even if the source is controlled by an attacker. Since the noise from the zener has no simple proof of it's entropy output rate, and it can vary over time, and because zener noise TRNGs have been known to be power-supply noise sensitive (not that your's is), having that second source gives me much more confidence in the device.
Turning both RNGs on only gets you a about half a bit/byte of extra entropy - but it is a great belt and braces sort of thing, makes it much harder to attack, especially since the sampling clock inside the device for both sources is not visible eternally
Remember we don't use the output data directly, we mix it into the kernel's entropy pool (where it's whitened)
I don't care how trustworthy everyone involved is or how closely we all look at it.
"Shouldn't an HW RNG NOT have any secondary communication method built in?"
Yes, that would indeed be a best practice.
Seriously. A radio. And not just any radio, but a software programmable, general purpose 802.x radio with a published spec, etc.
Also, this concern about the radio requires someone to 1) hack the TRNG, and 2) have a nearby receiver. At that point, they probably could more easily just PWN your system, and forget about the TRNG. Paul is doing some clever things to make it very hard to hack his firmware, but a keyboard logger is still easy for an attacker with physical access, as is any number of attacks.
Shouldn't an HW RNG NOT have any secondary communication method built in?
I am guessing you guys added that because that's the platform you're working with for your IOT project, but it just seems a little overkill to me. The diode data acquisition and the USB comms could be easily done using any Cortex-M0 type micro.