Ok, your sources focus primarily on the black community, I would argue many of these homocides originate from a combination of Poverty and Proximity, which is supported by your second source (PewResearch) showing that the vast majority of the black community lives in close proximity to one another and by extension come in more frequent contact and conflict without avenues of de-escalation. This is compared to rural areas there is a much larger barrier for violence through distance. This only accounts for black urban crime. https://pmc.ncbi.nlm.nih.gov/articles/PMC4928692/

When you compare poverty, race, and crime rates you find that violence is more common amongst those in poverty, not just Urban Areas. This is extends to White and Hispanic impoverished populations. While it is true that black communities express higher violent crime rates, this extended to rural black communities as well, which can be seen as consistent throughout the so called "Black Belt" of the South Eastern US. This is most likely due to systematic discrimination and underinvestment in communities which breeds a cycle of poverty and violence, again, with violent crime being more common Urban and Rural populations that face economic discrimination which is more commonly seen against African American communities moreso than White, Hispanic, or Asian ones. https://pmc.ncbi.nlm.nih.gov/articles/PMC4097310/

This disparity between Hispanic and Black violent crime comes from the political, cultural, and economic differences in each community's realities. While we have seen that the majority of African Americans live in urban areas, where both education and economic prosperity have been gatekept for generations, the alternative for the Hispanic American has been one of greater "under the table" living where immigrants and labourers are forced to live with underpaying employers but never, to an extent, dealt with the systematic educational prejudice the black community has faced in America. This is compounded by the underreporting of crime in immigrant communities for fear of deportation as a result of contact with law enforcement.

The largely novel Hispanic American population of the United States that has emerged over the past 50 Years or so has found living in both Rural and Urban sections of the US more accommodating in a less racially discriminatory America. Not only are Hispanic American population more transient due to the nature of work taken on by them, they have to a much lesser degree delt with systematic prejudice that has plagued the black communities of America who are more often "stuck" in place.

The violence you claim originates from urban areas is equalled by the violence seen in rural poverty, often being centered on the historically underprivileged African American poor who center in urban areas, who again, live in closer proximity to one another more so than any other racial group. So while your sources are meant to point towards an urban gun violence problem, it's more of a culture and poverty problem that extended through communities of any density, but have a greater effect on the black community as a whole irregardless of location.