Assuming that ISO in a DSLR is a 'fake' figure, matching the speeds of wet film & that as everything is calculated digitally, the 'best' calculation is 'no calculation at all'.
Is it a given that the lowest ISO on a camera is the one with no additional amplification or attenuation, or could that vary by make/model?
When I'm shooting under controlled conditions, where I'm in full control of all aspects including the lighting, then I tend to set my camera up at ISO 100 [the lowest it will go] & work from there. I set Aperture to give me my required DoF, exposure high enough to not need extraordinary measures to avoid shake; then I adjust my lighting until I'm in the zone.
Though I'm in full manual, including sometimes focus, for focus-stacked shots, I guess this method could be considered "ISO Preferred"
My camera is a Nikon D5500 & searching the reference manual would seem to give no absolute data, but does give hints that in auto modes such as Aperture Preferred that the camera will attempt to default to 100 if it can.
I didn't want this question to solely concentrate on a single camera model, though, so if there is any general guideline which would cover other models I imagine it would be more useful to future searchers.
As the D5500 has no separate, switch-enabled, ultra-low or ultra-high ISO setting, I am also guessing that perhaps these modes on other cameras do involve an extra amplification or attenuation stage, which a consumer camera may not have.