It's quite a large study (without any peer review btw) and I can't be bothered to get into reading much of the graphs so maybe I'm missing some important details to explain it away but I did find it rather odd that whenever someone in the comments on that site brought up the overall social stigma that surrounds black people in American society, the author often outright disagrees with its significance largely brushes it off as unimportant to his overall study but I really don't understand how that's the case? I clearly understand that measuring stigma isn't really possible but that doesn't mean it doesn't play a role and I feel that it explains a lot. Hundreds of years of slavery largely practiced on one ethnic group followed by intense segregation is going to predispose many people to certain outlooks on other groups of people. Stereotypes will be perpetuated, cycles will be repeated, etc.. Sure, it's clear that modern day economic factors don't explain the significant disparity in black crime rates (if we ignore the last point you mentioned) but modern day economic factors haven't really existed for American black folk for very long and they don't eliminate everything that has come before that may lead to modern black communities and culture having increased crime/homicide rates.

Look! The historically and actively stigmatized and disenfranchised group of people are just now able to be successful and have the means to live a well off life which means that it simply makes no sense that they would have higher violent crime rates than groups of people who descend from substantially less persecuted backgrounds!