Confusing errors reported when db-sync starts

When user starts db-sync, one of the geodiff calls produces a bunch of errors that are reported to the user. But these errors are not actual problems, and they just confuse users into thinking that something went wrong. I believe the failing queries are coming from libgpkg library, it would be good to find a way how to silence them:

GEODIFF: Error: SQLITE3: (1)no such table: main.gpkg_contents in "SELECT count(*) FROM "main".gpkg_contents WHERE data_type LIKE 'features'"
Error: SQLITE3: (1)no such table: main.gpkg_contents in "SELECT count(*) FROM "main".gpkg_contents WHERE data_type LIKE 'tiles'"
Error: SQLITE3: (1)no such table: main.gpkg_contents in "SELECT count(*) FROM "main".gpkg_contents WHERE data_type LIKE 'tiles'"
Error: SQLITE3: (1)no such table: main.gpkg_contents in "SELECT count(*) FROM "main".gpkg_contents WHERE data_type LIKE 'features'"
Error: SQLITE3: (1)no such table: main.gpkg_contents in "SELECT count(*) FROM "main".gpkg_contents WHERE data_type LIKE 'tiles'"
Error: SQLITE3: (1)no such table: main.gpkg_contents in "SELECT count(*) FROM "main".gpkg_contents WHERE data_type LIKE 'tiles'"
Error: SQLITE3: (1)no such table: main.gpkg_contents in "SELECT count(*) FROM "main".gpkg_contents WHERE data_type LIKE 'features'"
Error: SQLITE3: (1)no such table: main.gpkg_contents in "SELECT count(*) FROM "main".gpkg_contents WHERE data_type LIKE 'tiles'"
Error: SQLITE3: (1)no such table: main.gpkg_contents in "SELECT count(*) FROM "main".gpkg_contents WHERE data_type LIKE 'tiles'"

Start by reproducing the errors when db-sync starts, then trace the geodiff calls suspected of using libgpkg and emitting the SQLite messages. Identify whether the missing gpkg_contents queries are expected during startup, and verify that expected conditions are no longer reported as user-facing errors while genuine failures remain visible.