Change apk name with Gradle

As CommonsWare wrote in his comment, you should call appendVersionNameVersionCode only for staging variants. You can easily do that, just slightly modify your appendVersionNameVersionCode method, for example:

def appendVersionNameVersionCode(variant, defaultConfig) {
    //check if staging variant
    if(variant.name == android.buildTypes.staging.name){
        if(variant.zipAlign) {
            def file = variant.outputFile
            def fileName = file.name.replace(".apk", "-" + defaultConfig.versionName + "-" + defaultConfig.versionCode + ".apk")
            variant.outputFile = new File(file.parent, fileName)
        }

    def file = variant.packageApplication.outputFile
    def fileName = file.name.replace(".apk", "-" + defaultConfig.versionName + "-" + defaultConfig.versionCode + ".apk")
    variant.packageApplication.outputFile = new File(file.parent, fileName)
    }
}