Not sure I know exactly what you're getting at...you can 'popup' stuff with Javascript:
if ($_POST['submit'] {
echo '<script language=\"javascript\" type=\"text/javascript\">
<!--
alert(\"Changes have been saved...\")
--->
</script>';
}
---but, you are saying that changes have definitely been saved, cause you're doing it with PHP from the server, and testing the reception of at least one form item. It's gonna require that the server serve a page of some kind, is it not?
That's SS, there is no other way with PHP. If "things look messy", why not set up a script that is its own handler and have meaningful content in addition to status messages?