Just to be clear, they are using an automated code generator just to generate the machine-level instructions. They are still using MATLAB and other tools to work out the control algorithms in simulation.
Ummm, usually a code-generator has only so many different things it's expected to handle. Some human creates a template for a given situation, then when that situation arises the code is inserted into the final project. The idea that once a chunk of code has been proven to be correct, it will always be correct, has never quite worked out so far. Template writers (aka programmers) are usually around somewhere...