After reading and trying various functions, I couldn't find one that correctly parses all the configurations, strips any left-over html tag and converts special characters into UTF8 (e.g. ' into '), so I created my own by improving on the existing ones:

function phpinfo2array() {
    $entitiesToUtf8 = function($input) {
        // http://php.net/manual/en/function.html-entity-decode.php#104617
        return preg_replace_callback("/(&#[0-9]+;)/", function($m) { return mb_convert_encoding($m[1], "UTF-8", "HTML-ENTITIES"); }, $input);
    };
    $plainText = function($input) use ($entitiesToUtf8) {
        return trim(html_entity_decode($entitiesToUtf8(strip_tags($input))));
    };
    $titlePlainText = function($input) use ($plainText) {
        return '# '.$plainText($input);
    };
    
    ob_start();
    phpinfo(-1);
    
    $phpinfo = array('phpinfo' => array());

    // Strip everything after the <h1>Configuration</h1> tag (other h1's)
    if (!preg_match('#(.*<h1[^>]*>\s*Configuration.*)<h1#s', ob_get_clean(), $matches)) {
        return array();
    }
    
    $input = $matches[1];
    $matches = array();

    if(preg_match_all(
        '#(?:<h2.*?>(?:<a.*?>)?(.*?)(?:<\/a>)?<\/h2>)|'.
        '(?:<tr.*?><t[hd].*?>(.*?)\s*</t[hd]>(?:<t[hd].*?>(.*?)\s*</t[hd]>(?:<t[hd].*?>(.*?)\s*</t[hd]>)?)?</tr>)#s',
        $input, 
        $matches, 
        PREG_SET_ORDER
    )) {
        foreach ($matches as $match) {
            $fn = strpos($match[0], '<th') === false ? $plainText : $titlePlainText;
            if (strlen($match[1])) {
                $phpinfo[$match[1]] = array();
            } elseif (isset($match[3])) {
                $keys1 = array_keys($phpinfo);
                $phpinfo[end($keys1)][$fn($match[2])] = isset($match[4]) ? array($fn($match[3]), $fn($match[4])) : $fn($match[3]);
            } else {
                $keys1 = array_keys($phpinfo);
                $phpinfo[end($keys1)][] = $fn($match[2]);
            }

        }
    }
    
    return $phpinfo;
}

The output looks something like this (note the headers are also included but are prefixed with '# ', e.g. '# Directive'):

Array
(
    [phpinfo] => Array
        (
            [0] => PHP Version 5.6.5
            [System] => Darwin Calins-MBP 15.0.0 Darwin Kernel Version 15.0.0: Wed Aug 26 19:41:34 PDT 2015; root:xnu-3247.1.106~5/RELEASE_X86_64 x86_64
            [Build Date] => Feb 19 2015 18:34:18
            [Registered Stream Socket Transports] => tcp, udp, unix, udg, ssl, sslv3, sslv2, tls, tlsv1.0
            [Registered Stream Filters] => zlib.*, bzip2.*, convert.iconv.*, string.rot13, string.toupper, string.tolower, string.strip_tags, convert.*, consumed, dechunk
            [1] => This program makes use of the Zend Scripting Language Engine:Zend Engine...
        )

    [apache2handler] => Array
        (
            [Apache Version] => Apache/2.4.16 (Unix) PHP/5.6.5 OpenSSL/0.9.8zg
            [Apache API Version] => 20120211
            [Server Administrator] => webmaster@dummy-host2.example.com
            [Hostname:Port] => sitestacker.local:0
            [# Directive] => Array
                (
                    [0] => # Local Value
                    [1] => # Master Value
                )

            [engine] => Array
                (
                    [0] => 1
                    [1] => 1
                )

            [last_modified] => Array
                (
                    [0] => 0
                    [1] => 0
                )