The author's claim that "a CMake-generated project cannot possibly be the final say" is so incorrect that I am not surprising that he found CMake frustrating. It is quite the opposite; if you ever find yourself manually editing the generated project files for any reason other than debugging build-system issues you're doing it wrong and are going to have a very bad time. You must always find a way to express the thing you need within the CMakeFiles.txt, which sometimes unfortunately requires awful hacks.
Amusingly the SO question he links to as evidence that editing the generated project file is required now has an answer saying how to do it properly...