CMake can't do everything autotools does, but the stuff autotools does which CMake doesn't isn't relevant anymore in today's world.

The fundamental curse of build systems is that they are inherently complex beasts that hardly anybody has to work with full-time, and so hardly anybody learns them to the necessary level of detail.

The only way out of this is to simplify the problem space. Sometimes for real (by reducing the number of operating systems and CPU architectures that are relevant -- e.g. CMake vs. Autotools) and sometimes by somewhat artificially restricting yourself to a specific niche (e.g. Cargo).