Hi @Thanatomanic , first of all congratulations for your work on the histogram, and for your final question, that has not an easy answer really. I’m just trying to learn RawTherapee, trying to get the most out it it, and we can safely assume I am in the initial stage of the learning process, still having myself a lot of doubts about the real usage of a raw converter. Moreover it takes me some time to write in English, for all this I can’t give you a thorough answer all at once (provided yours wasn’t just a rethoric question).
So to begin with your question, to me a histogram should be visually descriptive. I would say I would exclude a logarithmic y-axis which I think gives a wrong visual idea of pixel distribuition, and of course you can avoid a flattening of the remaining levels by truncating vertical spikes (the truncated spike is a good visual indicator too, you don’t really need to know the exact pixel count).
To beat you: But you can ignore it by using only linear scaling, is not a good point to me. 
Then there are other things, of course.