What you describe is certainly a danger, but there is the opposite danger, which is that we ascribe to race things that are actually random, and the intermediate case where we correctly note that race has at some point had something to do with it, but we get completely wrong when and/or what the causal process was.
I don't know the story with the waste plants, so I don't know what the reality is, but let's consider two extremely different scenarios. (1) Black people are congregated into particular neighborhoods, then waste plants are put there because the objections and health of black people don't count, and this also causes financial harm to the black people who live there by depressing home values; or (2) a waste plant is put in a neighborhood, which depresses the value of homes in the area, making them affordable to black people suffering from financial hardship, who preferentially move there because some home is better than none.
In each case, there is an underlying disparity that is of concern, but in the first case, the people locating the plant are at fault for pernicious attitudes, whereas in the second case the people locating the plant are completely blameless. It's really really important to get this right if your solution is, for instance, better oversight of how we locate waste plants.
The court shouldn't, in cases like that, require each person to be treated individually because of course that's not how decisions about infrastructure are made. You can't just look at the disparity and go, "Oh, discrimination in waste plant location!" because as the scenario above shows, you can end up with a racial disparity without any direct connection to prejudicial selection of waste plant location. However, you don't have to go all the way down to the individual level in order to resolve the issue! You just need to go into the historical data, dig a little deeper and see what conditions were when the plant was placed there. 95% disparity seems like a really bright red flag. If you did go into the historical data, I bet you'd find that the placement locations were not impartial (in effect, even if at this point you couldn't prove intent). It's reasonable for a court to ask for the right group-level statistical data, not just "somehow it ended up wrong, therefore WasteCo is at fault".
It is not reasonable for the court to get that group level data and say, "Well, yeah, statistically there's no doubt that this was discrimination, but individually we can't tell because there's no statistical power there, so nothing wrong happened, and no remediation is necessary." That's just boneheadedly innumerate.
In contrast, individual consideration is how decisions about college admission are made. You don't admit a neighborhood, you admit a person. So it's not really clear that your point is terribly relevant to dczook's analysis.