The system most certainly accounts for it. I can't speak for state institutions as I do not know, but private schools are most certainly willing to let a black kid in with lower scores.
I am now coaching the smartest travel baseball team in the country, the East Cobb Patriots (that may be too much info, but oh well.) Our average ACT is a 31 and average SAT is 1320. We have former players currently on every ivy league roster and a kid at Cal Tech. We had a black kid this summer that made an 1180 SAT. This is far from good enough for top 25 schools, but yet almost every one said that they could get him. I was talking to a recruiting coordinator and an academically elite power 5 school. We were discussing the academic side of recruiting and he looks at me and says "Coach, you have it all wrong. We don't go after premier grades kids. We go to inner cities and sign those kids because it is easier for us to get them into school."
To make a long story short, schools most certainly account for the fact that black kids, for whatever reason, score lower on a whole.