Because the system tools are the published API!

Using the system tools will allow the software to work unchanged if the passwd database backend is not flat files. Perhaps more importantly in the case that you do not expect to be using anything other than flat files as the backend, the system tools will respect all the conventions regarding updates to /etc/passwd and /etc/shadow like making a backup file after changes (/etc/opasswd, maybe), file locking, and use of MD5 passwords versus traditional crypt, all of which you might not know about and which may vary from system to system.

Using a pty is a pain, but it's worth it.