Those codes have been part of Redux for years and wp.org never complained. I’m afraid we can’t change the inner workings of Redux and break backward compatibility with themes not offered on wp.org to satisfy wp.org and their ever changing demands.
However, since you are embedding, you can modify those files. First, make sure you have the latest Redux. The line numbers you indicated don’t match up with the latest version. In redux-core/inc/classes/class-redux-filesystem.php, locate the function
move_uploaded_file( string $file, string $destination, int $perms = null ) and delete the entire function. Redux does not use it anymore, but older projects may still use the function as part of our filesystem wrapper (and why the function still exists). Since you’re not using it, you can safely get rid of it.
wp.org’s other complaint has to do with the Redux templating system. We removed it last year, but some of the code was left behind for projects that used the system for backward compatibility. In the redux-templates/classes/class-template-overrides.php, you can safely delete all the EOD blocks. Change any $css variables that contained them to a blank string. Eventually, the legacy code will be removed in a future version.
Hope that helps.