I'm not sure, as this paper is very confusing in its style, but I think they try to modulate the load resistance connected to an antenna on the TX side. Since the open has a large real resistance (25k in their case), it's poorly impedance matched to the antenna and most of the noise powwr cannot be transferred to the antenna at 1.4 GHz they are using. 50 ohm load is well matched, hence the max noise power transfer to the antenna. This is all at TX.
I don't see a thermodynamic problem here. Noise modulation with switching is well known in electronics. Switched resistors and their noise is already analyzed. It is often in the context of noise parr of SNR though. They are using this noise modulation to transmit signals, which isn't too novel. I guess the transmit power is very low but this would be horrible for Shannon spectral efficiency because of the need for noise power detection, which cannot be instantenous.
I suspect GP's question is answered by the fact the system is not in thermal equilibrium. The view the antenna has is approx half of the sky whose temperature is far lower than room temp. Even indoors, the roof of your house is sufficiently transparent in RF that you are still seeing the sky behind.
If the same experiment was done in metal box with everything of constant temperature, I don't think it would be possible to transmit any bits.