/**
 * @param array $array
 * @param array $keyPath
 * @param $value
 *
 * @return array
 * @throws InvalidArgumentException
 */
function addValueToArrayByKeyPath ($array, $keyPath, $value) {

    if (!is_array($array)) throw new \InvalidArgumentException;

    $level =& $array;
    foreach ($keyPath as $key) {
        if (!array_key_exists($key, $level) or !is_array($level[$key])) {
            $level[$key] = [];
        }
        $level =& $level[$key];
    }
    $level = $value;

    return $array;

}

$array = [
    1 => [
        2 => [],
        9 => [],
    ]
];
$keyPath = [1, 2 ,3];


$array = addValueToArrayByKeyPath($array, $keyPath, 42);
var_dump($array);

/* output:
array (size=1)
  1 =>
    array (size=2)
      2 =>
        array (size=1)
          3 => int 42
      9 =>
        array (size=0)
          empty
*/