I'd say the biggest issue is the idea that widespread and institutionalized racism and racial violence was far more restricted, especially geographically, than it actually was.

The modern narrative is that racism and apartheid policies were mostly restricted to the south, where the worst examples existed. But while several of the most appalling aspects of institutionalized racism existed in the south, for the most part such racism was simply more visible because of the high black local population in such places, not because of an absence of racism elsewhere. Many cities outside of the south had racial exclusion laws, forbidding ownership of property in certain neighborhoods or in the entire city by blacks. And in many cases outlawing blacks from even spending the night in a city. While many unions excluded blacks from the best paying jobs in many desirable industries. To say nothing of the ubiquitous anti-miscegenation laws around the US. When there are only a handful of black people who might visit your city during the day and none who live there, it would be superfluous and unnecessary to segregate bathrooms or water fountains.

Segregation, oppression, and disenfranchisement of blacks (and latinos, and asians) existed nearly universally across the US, it was just more blatant and obvious in the south due to the presence of large black populations there.

These official legal policies were supplemented with private, quasi-legal, and extra-legal actions as well, even after the civil rights act was passed. Bankers made it nearly impossible for blacks to get mortgages for homes across "red lines" into neighborhoods blacks weren't supposed to be allowed in, which continued up through the 1980s in some capacity and still continues, though less so, even today. Aggressive or intrusive police attention made it clear to black visitors to cities when they weren't wanted, and encouraged them to move on. And terrorist activities from groups such as the KKK discouraged blacks from doing anything that might give them too high a profile.

Moreover, many examples of racist policies outside of the south were formulated to be a lot more clever and subtle than the blatant segregation of the south. For example, Robert Moses was a hugely powerful unelected urban planner in the New York City area during the mid to late 20th century. He made several key decisions which were designed to keep blacks from being able to travel to, work in, or migrate to certain areas, many of which are not obvious until revealed. For example, there are dozens of overpasses on Long Island parkways which are much lower than they would normally be expected to be, which was Moses' attempt to prevent buses (and thus blacks) from being able to get to the parks and beaches on Long Island. Similarly, he acquired right of ways for road building which were only narrow enough to allow for a road and would prevent the addition of future rail lines, despite it being trivial (and suggested) to allow the possibility.

Similarly, many public school systems throughout the country, even outside the south, had very difficult struggles to desegregate after the passage of the civil rights act, with some (such as Boston) coming under court control to ensure they actually carried through, and were met with popular grass roots protests by whites to stop the school desegregation.

Racism in the form of laws, policies, and practices that maintained white supremacy existed throughout the US. Many of them far less obvious and far more subtle than the open apartheid practiced in the ex-confederacy. That was reflective of the popular support for racist ideals that pervaded the America throughout most of the 20th century.