When adjusting the permissions for the Emby application user on a shared folder, try enabling the option to 'Inherit shared folder permissions'.
The option "Replace the permissions of all subdirectories with permissions of the folder" is set and it works on Plex Server. This is the alert message from Emby Server:
Exception of type 'SQLitePCL.pretty.SQLiteException' was thrown. at SQLitePCL.pretty.SQLiteDatabaseConnection.PrepareStatement(String sql, ReadOnlySpan`1& tail) at SQLitePCL.pretty.DatabaseConnection.PrepareStatement(IDatabaseConnection This, String sql) at Emby.Server.Implementations.Data.SqliteItemRepository.QueryItemsInTransaction[T](InternalItemsQuery query, IDatabaseConnection db, String[] columnsToSelect, Boolean filterColumns, String[] groupBy, Func`5 rowReaderFn, String methodName) at Emby.Server.Implementations.Data.SqliteItemRepository.QueryItemsInTransaction[T](InternalItemsQuery query, IDatabaseConnection db, String[] columnsToSelect, Boolean filterColumns, Func`5 rowReaderFn, String methodName) at Emby.Server.Implementations.Data.SqliteItemRepository.GetItemList(InternalItemsQuery query) at Emby.Server.Implementations.Library.LibraryManager.GetItemsResult(InternalItemsQuery query) at MediaBrowser.Controller.Entities.Folder.GetItemsInternal(InternalItemsQuery query) at MediaBrowser.Controller.Entities.AggregateFolder.GetItemsInternal(InternalItemsQuery query) at MediaBrowser.Controller.Entities.Folder.GetItems(InternalItemsQuery query) at MediaBrowser.Controller.Entities.Folder.GetChildren(InternalItemsQuery query) at MediaBrowser.Controller.Entities.Folder.GetChildrenForValidation() at Emby.Server.Implementations.Library.LibraryManager.ValidatePhysicalRoots(IProgress`1 progress, IDirectoryService directoryService, CancellationToken cancellationToken) at Emby.Server.Implementations.Library.LibraryManager.PerformLibraryValidation(IProgress`1 progress, CancellationToken cancellationToken) at Emby.Server.Implementations.Library.LibraryManager.ValidateMediaLibraryInternal(IProgress`1 progress, CancellationToken cancellationToken) at Emby.Server.Implementations.ScheduledTasks.ScheduledTaskWorker.ExecuteInternal(TaskOptions options)