The S3 Usage report converts each daily line item to the actual amount seen that day. This amount is rolled up to the month and then it is averaged which can result in differences due to rounding after the average is taken.
FlexReports, on the other hand, just sums up the line items.
These calculations should be close but due to rounding they will likely differ. At scale, when rounding affects a large number of buckets there would likely be a small difference.
Ultimately, the FlexReport result will likely be more accurate as it's pulling metrics directly from the bill without additional manipulation.