ISO-based denoise presets useless for iso-invariant cameras

In most cameras, no. Check photon for specifics.

OP:
I think there is an important distinction on your workflow. If you are using the camera metering to determine the shot exposure (shuttle speed and aperture), then selecting a higher ISO in the camera will negatively impact the captured data by the sensor. Why? At the higher ISO, the camera will meter and suggest a speed/aperture that actually allows less energy ( light + time) to reach the camera sensor. Therefore you will be capturing less information (less energy reaching the sensor) in from the shadow areas of the image. Therefore, keep the iso in the camera low, to capture more energy even if the image ends up looking “underexposed” in the camera, you can then use the software to amplify captured energy.

PS: in other words, how/where you meter matters. Try to get as much energy as possible without clipping the sensor signal.