By calibrating the light source to make the base a “balanced clear” with a maximum of 95% it appears the method is consistent with using the maximum range of the sensor for each color, which would also yield the best S/N for each color, what I referred above as the maximum range of the content.
The one time where that would fail I think is when the content negative is too dark (over exposed I think), in which case -as you describe- overriding it to clip the base and bring the “content base” to 95 percent would again yield the best S/N. There are cases where that override balance is not the same in the content as in the base, for example when the overexposed source light is of a different temperature than the correctly exposed portion, so it would be good to be able to override maintaining the content balance, and providing an override gain over the content balance for these scenarios.
In another threat someone was referring to automatically balancing using light. If the system provides a feature to select the base area to balance for, that can be accomplished. In essence the default area may be portions similar to what you described, with an override to select a specific portion to calibrate when needed.
In summary, keep the content range to the best 0-95 for each sensor, providing a similar quantization and S/N for each channel.
Unrelated, but appropriate to mention is another special case: the old content with a faded die. From what I seen, it results in a change of the curve for the color, the faded die shift the blacks (this is for reversal), but since the whites are whites, I don’t know if this issue can be better if adjusting the light… have to think about it. In this case, the noise would suffer too.
My guess is that if is non-reversal, adjusting for the content would address improve it… but have to think about it too.