An obvious example I have is CMake. I have seen so many people complaining about CMake being incomprehensible, refactoring it to make it terrible, even wrapping it in Makefiles (and then wrapping that in Dockerfiles). But the problem wasn't the original CMakeLists or a lack of comments in it. The problem was that those developers had absolutely no clue about how CMake works, and felt like they should spend a few hours modifying it instead of spending a few hours understanding it.
However, I do agree that sometimes there is a need for a comment because something is genuinely tricky. But that is rare enough that I call it "a comment" and not "literate programming".
As for convoluted, I don't find it harder than the other build systems I use.
Really the problem I have with CMake is the amount of terribly-written CMakeLists. The norm seems to be to not know the basics of CMake but to still write a mess and then complain about CMake. If people wrote C the way they write CMake, we wouldn't blame the language.