That document is quite old, and I'm sure he has gathered more experience over the years.
I could have a field day correcting him, expecially as on this page he is talking about security and starts by saying he's no expert on it. Well then sh*t up! :-)
He is worried about storing password in plaintext for CGI scripts, because if someone gets root permissions on your server, they can read the CGI scripts.
Hellooo! if they can get your server's root permissions, you have a lot more to worry about than a few passwords to some database. giggle
Putting everything behind a firewall because databases like Informix don't have proper security? giggle did he ever work with informix at all? Or unix for that matter?
Oh well, enough of this, he's not here to defend himself, so I'll just conclude that at the time he wrote this document he clearly was 'not an expert' and he probably shouldn't have written it.