For 99% of our jobs, we will always want to flatten the files, and for new jobs, we prefer this option is already checked just to simplify the setup. We are working to encourage everyone to use the ftp publish functionality, so any little things like that are helpful.

Note that I have implemented this feature for the FTP-Publisher Plugin, but since your plugin is under active development, it would be nice if it had all the features I need, and we could migrate to it once we move to a newer version of Jenkins that your plugin will support.

See https://wiki.jenkins-ci.org/display/JENKINS/FTP-Publisher+Plugin