I have a webapp that needs to process the URI to find if a page exists in a database. I have no problem directing the URI to the app with .htaccess:
Options +Fo
I don't think you can "hand it back" to Apache, but you can send the appropriate HTTP header and then explicitly include your 404 file like this:
if (! $exists) {
header("HTTP/1.0 404 Not Found");
include_once("404.php");
exit;
}
Update
PHP 5.4 introduced the http_response_code function which makes this a little easier to remember.
if (! $exists) {
http_response_code(404);
include_once("404.php");
exit;
}