Why terrifying? Sounds like he saw that the structure of much of what he was doing was boilerplate and created a bespoke code generator to save himself time. As long as the resulting queries are readable and effective I don't see a problem. Unless I'm missing something, understanding his code generator is not (necessarily) a pre-requisite for understanding the resulting code.
Because you're leaving an unmaintainable mess. Nobody else can rationalise the code aside himself. It's harder to debug because even he cannot account for every edge case his regex might throw up -- which also makes it less secure. Also regex is comparatively slow so transforming an SQL query using multiple regex search and replace patterns is not the way to write hot code hit by literally millions of visitors each hour.
> understanding his code generator is not (necessarily) a pre-requisite for understanding the resulting code.
Oh it absolutely is if you want maintainable and secure code. I get some situations call for complexity but when you're generating SQL on a public facing web application with a centralised database backend, you want to be damn sure you can rationalise the SQL being generated. The best ways of doing that is to either not to try to be too clever with your generation (KISS) or to put your confidence into an established and well tested existing ORM or equivalent.