If the second contains the System backups it would include those of stopped apps, where a backup was made there (since otherwise the backup data simply wouldn't be there). But I agree this is not great to migrate. I guess for now you would have to start the app, make a full system backup on the scondary backup site and then stop the app again.
The code for retrieving backup data for integrity check depeneds on format and storage type. Memory consumption is hard to predict, so presumably S3 with some kind of data on that storage just gets it over the 400MB