People tend to focus on things singularly. The black on black crime meme is a way not to discuss police killings. If certain media can get you to look over here, you won't see or think about what is going on over there.
All crime is intra-racial (internal to race) because all crime are crimes of convenience, crimes among people close to one another. So the rates of crime within a race will always be higher than rate between races. That has nothing to do with which one is a bigger problem, but who people tend to live among. It is a stat that tells us nothing, except perhaps as an illustration of how segregated our society still is.
Numbers are funny things and can easily mislead. Don't be misled.
You're correct that intra-race crime rates are higher, because crime is a form of interactions and all forms of interaction are more likely between people in closer proximity to each other.
However, you are quite incorrect that this is not relevant for is the issue of police shootings. Proximity and who one is around plays as big a role in cop-civilian interactions and conflicts as it does everywhere else. Most cops spend much more time around, interacting with, and in conflict with blacks than whites as a proportion of the population of these groups. This means that when a cop does something wrong (whether accidentally or otherwise) the victim of this action is disproportionately more likely to be black. IOW, cops are more likely to shoot a black person for the same reason that black people are more likely to shoot a black person. It is the communities they are in and the people they are around. In addition, black people in a heavily black area are more likely to be assaulted than in a white area. The same is true for cops. If a cop spends an 8 hour shift in a black area vs. white area, they will encounter more crime, more serious crimes, more illegal guns, and more conflict and aggression when they arrive on the scene. As it would with all rational people, this puts cops more on "alert", more cautious, and suspicious when they are in these areas. What all this means is that much of the greater rates of cop shootings involving blacks is due to the same statistical and contextual factors that make blacks more likely to shoot another black than a white, and black victims of shootings more likely to be shot by another black person than a white person.
So, the question is then, why are cops spending so much time in black areas? The answer is that this are much higher crime areas, in large part because they are low SES areas. Thus, the high black-on-black crime rate is also highly relevant to this question. That high rate is what brings cops to the neighborhood so often, and the same proximity issue that makes intra-race crime rates higher also makes crimes by cop rates higher in relation to blacks. Plus, the objectively higher probability that a cop will encounter a threat, violence, or an illegal gun in black neighborhoods makes them more likely to commit a judgment error biased in favor of false-positives in threat assessment.
If anti-cop activists would acknowledge these undeniable statistical realities rather than wrongly interpreting every stat and every instance as evidence of racism, then we might be able to make progress in targeting actual instances of racism based police abuse, and in more generally reducing police abuse and errors that are not rooted in racism.