Ok, but that decision would have to be made by the project maintainer, in this case Google, not the person using Bazel to compile protobuf. (And not particular to Bazel -- a developer can make any build system effectively hermetic by vendoring everything.)

In my view the challenge here is that a dependency changes (e.g. /usr/include/stdio.h is upgraded by the system package manager, or two users sharing a cache have different versions of a system library) and Bazel doesn't realize that it needs to rebuild. It would be a pretty heavy hammer if the way to fix that requires every OSS project to include the whole user-space OS (C++ compiler, system headers, libraries) in the repo or via submodule and then be careful that no include path or any part of the build system accidentally references any header or library outside the repository.

And maybe this issue just doesn't need to be fixed (it's not like automake produces build rules that explicitly depend on system headers either!) -- my quibble was with the notion that Bazel, unlike CMake or whatever, provides fully hermetic builds, or tracks dependencies carefully enough to provide an organization-wide build cache across diversely configured/upgraded systems.