The difference between these two reports is coming from Past Students. Past Students are included in the Student Body Diversity - By Year report because those students were enrolled in the school at some point during the year. We don't have them in the Student Body Diversity - By Level or Grade report because they currently do not have an active level or grade for the report to pick them up from.
The two reports are designed for different purposes, and the Student Body Diversity report is better used as a snapshot of current enrollments, rather than historical enrollments. It is best to use the Student Body Diversity-By Year report when you need diversity information for past years.