1. The file size difference after migration is an expected behavior for small office files (in this case versions). Office files are zip of XML and during the migration process (by any API) it may get a few kb more or less depending on file structure, text, properties, metadata, scripts, format etc but if you open files in UI/browser you will see they are same.
2. In a library with versioning enabled, the "Overwrite if File Exists" option performs an overwrite on files already in SharePoint. SharePoint will append these to the list as new versions.