The article suggests writing explicit rules to check for changes in the toolchain.

These dependencies can be recorded automatically with LD_PRELOAD. LD_PRELOAD can redefine functions such as fopen and let you record what files are read when running e.g. cc.

This makes it feasible to record the entire relevant state of a system, files and environment variables, at build time.

An argument in favor of checksums is the use of build caches. Switching between branches on large codebases triggers a lot of rebuilds. With a build cache, that can be avoided. SCons is a build system that uses such a cache.