Internally the app & daemon use qwebdav, and there is no simple and bullet proof way to find duplicates (for example, via file hashes) from arbirtrary locations via the webdav protocol. It would just upload your local ~/Pictures directory to the remote /Jolla directory. In case a remote file has the same name/relative path locally we assume that it was uploaded by the backup daemon and don't overwrite it. After all, you usually don't edit pictures on the phone, when you "edit" them via the Gallery app it creates a new file and thats it.
1) Already changeable from within the application settings 2) Already the case, upload only happens via WIFI 3) I could add UI to the settings for that, it certainly is easy to add.