Is there an argument to be made that it doesn't matter whether or not he is right in the case that you want to reduce incarcerations and that this is muddying the water?

Laws get passed by support, support is gained by attention and focus. War on drugs is obvious in the population, the decriminalization of marijuana is obviously happening. The response that you've pointed out from the article here on HN supports the idea that many people have a strong belief that mandatory minimum sentences and a tough of drugs stance has helped to flood the prison systems.

Now you say the author appears to be against the drug war and against mass incarceration. During his research he sees that drug related incarcerations aren't nearly as large a problem as the increase in seeking felony charges. He writes this paper, says hey look at this other problem inside a problem!

But he doesn't make it clear, and I judge this from the comments here, that he thinks the initial problems exist. Thus positioning himself against them because the counter arguments will be made by the opponents of the end to the drug war, and the people who say mass incarceration isn't an issue will point to this paper and say: "See the drugs aren't the problem the violence is increasing, therefore we suggest that your honor not repeal prohibition"

You want the deck stacked in your favor, the mass opinion needs to be on your side, to suggest alternatives is to weaken the force trying to repeal prohibition. To weaken the arguments to the point where no decision can be made is still winning for the people wanting to keep the war on drugs going and the incarceration rate up. Indecision is loss, you'd want to have a unified voice to make the change happen.

That you've highlighted these points so much is commendable, but the author should have done that work for you from the outset. You are relying on people giving the cognitive effort required to come to their own conclusions. That is a mistake when you are dealing with more then on person, and we want everyone to agree to end the drug war right?

Thus the way to do that, even if the author sees this other problem in a problem, is to put his weight and effort into reinforcing the existing propositions. Then once those propositions are past, which is incredibly hard, highlight the other problem areas. Start from the outside in and from the positions with the most support. The war on drugs appears to be weakening, but it isn't done, and the mass opinion can't handle a distraction, which gives power to the incumbents.

So he is right, felony handouts are the bigger problem by percentage. Try and argue that assault with a deadly weapon charge should see a reduced sentence, or any other more grevious charge, and you'll be fighting the "think of the children crowd", the "why do you want the murderer of my child to go free parent". Right now the power is building to reduce the war on drugs, which would reduce incarcerations by a measurable amount. Put the focus there, then continue with a winning moment in the end of prohibition to say "look here there is another terrible atrocity, lets keep making America better!"

There is more than changing laws to being right, and I think that is why you're seeing the response you've highlighted in your multiple comments.