Note, for ReflectionClass::getMethods() not all methods in a final class are final, just the ones that have explicit modifier.
If you want to use an and operator for the filter, here is a simple implementation
<?php
final class Apple {
    public function publicMethod() { }
    public final function publicFinalMethod() { }
    protected final function protectedFinalMethod() { }
    private static function privateStaticMethod() { }
}

class MyReflection extends ReflectionClass {
    public function __construct($argument) {
        parent::__construct($argument);
    }
    
    /**
     * (non-PHPdoc)
     * @see ReflectionClass::getMethods()
     */
    public function getMethods($filter = null, $useAndOperator = true) {
        if ($useAndOperator !== true) {
            return parent::getMethods($filter);
        }
        
        $methods = parent::getMethods($filter);
        $results = array();
        
        foreach ($methods as $method) {
            if (($method->getModifiers() & $filter) === $filter) {
                $results[] = $method;
            }
        }
        
        return $results;
    }
}

$class = new MyReflection('Apple');
$methods = $class->getMethods(ReflectionMethod::IS_FINAL | ReflectionMethod::IS_PUBLIC);
var_dump($methods);

$methods = $class->getMethods(ReflectionMethod::IS_FINAL | ReflectionMethod::IS_PUBLIC, false);
var_dump($methods);
?>

Result:
array(1) {
  [0]=>
  object(ReflectionMethod)#4 (2) {
    ["name"]=>
    string(17) "publicFinalMethod"
    ["class"]=>
    string(5) "Apple"
  }
}

array(3) {
  [0]=>
  &object(ReflectionMethod)#5 (2) {
    ["name"]=>
    string(12) "publicMethod"
    ["class"]=>
    string(5) "Apple"
  }
  [1]=>
  &object(ReflectionMethod)#3 (2) {
    ["name"]=>
    string(17) "publicFinalMethod"
    ["class"]=>
    string(5) "Apple"
  }
  [2]=>
  &object(ReflectionMethod)#6 (2) {
    ["name"]=>
    string(20) "protectedFinalMethod"
    ["class"]=>
    string(5) "Apple"
  }
}

ReflectionClass::getMethods() sorts the methods by class (lowest in the inheritance tree first) then by the order they are defined in the class definition:

<?php
class A {
    public function method1() {
        
    }
    
    public function method2() {
        
    }
}

class B extends A {

    public function method3() {

    }

    public function method4() {

    }
}

$class = new ReflectionClass('B');
print_r($class->getMethods());
?>

This will output:

Array
(
    [0] => ReflectionMethod Object
        (
            [name] => method3
            [class] => B
        )

    [1] => ReflectionMethod Object
        (
            [name] => method4
            [class] => B
        )

    [2] => ReflectionMethod Object
        (
            [name] => method1
            [class] => A
        )

    [3] => ReflectionMethod Object
        (
            [name] => method2
            [class] => A
        )

)

Method ReflectionClass::getMethods doesn't work constantly across different versions of PHP. For following code piece

<?php
class Dummy implements Iterator
{
    public function current () {}
    public function next () {}
    public function key () {}
    public function valid () {}
    public function rewind () {}
}

$reflection = new ReflectionClass('Dummy');
$aMethods = $reflection->getMethods();
echo '# of methods: ', count($aMethods), "\n";
?>

, it outputs "# of methods: 10" on PHP 5.2.14 and PHP 5.2.17, including all methods defined in the class itself and in the interface no matter if a method has been implemented or overridden; however, it returns "# of methods: 5" on PHP 5.3.5. Based on some other tests did by my colleagues, I assume it also returns "# of methods: 5" on PHP 5.2.10 and PHP 5.3.6.