Adding a series resistor of ~100 ohms with the fan lead reduces the fan induced noise and also the audible noise. CH1 is still more noisy than CH2, with mostly noise spikes from the XL6012 switching (44mvpp with 370uv SD), while CH2 has little noise spikes and lower overall (8mvpp with 300uv SD). There's still good airflow, but much quieter fan, and I don't expect any temperature related issues.
Here's a couple images of the added series resistor, used a male and female HX-2 style connection like the fan uses, and this plugs into the fan connector and PCB connector as shown. Very simple and doesn't alter the DPA-2698 fan cable or PCB.
Best,