[_jal]

> One was just a collection of PHP scripts that would trigger SQL queries.

Yes, I've had to build a system like that (Java, but same diff.)

This model is popular in particular with banks, because they can split sensitive responsibilities in a way that makes sense to them.

It works fine if you have good communications between developers and DBAs. If you don't... well, I won't have to suggest finding another gig, you already want to.