I might have to make clean with CMake after a distro compiler upgrade where the compiler is behind the same symlink or something, dunno, I don't really remember doing that. Otherwise, no make clean because I understand how CMake works. Really, I do. Including with generated code and all that. Wildcards in CMakeLists.txt are misuse.

System libraries are intentionally disregarded as possibly changed dependencies, that is a design decision that most build systems make. System libraries are not supposed to change in binary incompatible ways without a major version upgrade.

Your last point is about reproducible builds, which is a different topic.