There is a discrepancy on column collation between kohastructure.sql and upgraded databases. One example is the "localization" table. Upgraded databases will have "utf8_unicode_ci" set for column collation and table collation. However, kohastructure.sql only has it at the table level. If you're using an audit script like in bug 34064, this difference will show up. While it's a minor difference, it's a noisy difference and a difference nonetheless.