The code in the first exemple doesn't work properly without the flag  FilesystemIterator::SKIP_DOTS in the RecursiveDirectoryIterator (on a linux filesystem).
So, to build a tar with a phar, I do (with two level of iteration here) :
            $pharTar = new \PharData($contentTar.".tar");
            $firstLevelIterator = new \DirectoryIterator($this->inputPath);
            foreach ($firstLevelIterator as $fileInfo) {
                /* @var \SplFileInfo $fileInfo */
                if (in_array($fileInfo->getFilename(), $allowedDirectory)) {
                    $recursiveDirectoryIterator = new \RecursiveDirectoryIterator(
                        $this->inputPath . DIRECTORY_SEPARATOR . $fileInfo->getFilename(), \FilesystemIterator::SKIP_DOTS);
                    $pharTar->buildFromIterator(new \RecursiveIteratorIterator($recursiveDirectoryIterator), $this->inputPath);
                }
            }