If a person has access to your filesystem, your server is compromised and it doesn't matter where you keep your files - they'll still be able to find the file. If the server is compromised, and it also holds your database, then it doesn't matter if they can read your credentials - they have access to your database anyway. So, there's no real need to worry about hiding your credentials from someone that has access to your filesystem.
One legitimate, but in my opinion overly paranoid, concern could be what happens if the Phalcon AND mod_rewrite modules both die, but Apache keeps running. In that case, a web user could have access to the config.php file and have it delivered as raw text. However, the likelihood of both those modules not running, and Apache still working, is practically zero. It may even be impossible - I'm not that much of an Apache expert. Even if it did happen and your credentials got out, you could (and should) lock down your database to only be accessible from known IPs, or from "localhost".
In short, don't worry about it, just make sure the database itself is secure.