bazel missing include directory in bazel-out - c++

Question

I've noticed that when I try to build a c++ project with some flags, e.g., "-Wall -Wmissing-include-dirs", bazel gives a missing include directory.
The project structure is the following
root
├── src
│ ├── CMakeLists.txt
│ ├── BUILD.bazel
│ └── main.cpp
├── CMakeLists.txt
├── README.md
└── WORKSPACE
src/main.cpp
#include<iostream>
int main()
{
std::cout << "Compiled\n";
return 0;
}
src/CMakeLists.txt
cmake_minimum_required(VERSION 3.10)
project(main)
set(CMAKE_CXX_FLAGS "-Wall -Wmissing-include-dirs -Ipath/that/doesnt/exist")
set(SOURCES main.cpp)
add_executable( main ${SOURCES})
src/BUILD.bazel
cc_binary(
name = "main",
srcs = ["main.cpp"],
copts = ["-Ipath/that/doesnt/exist -Wall -Wmissing-include-dirs"],
)
When compiling main.cpp with cmake (mkdir build && cd build && cmake .. && make), I see an expected warning for path/that/doesnt/exist (since it doesn't exist), e.g.,
cc1plus: warning: path/that/doesnt/exist: No such file or directory [-Wmissing-include-dirs]
but when I compile with bazel (bazel build //src:main) I get an additional missing include
cc1plus: warning: path/that/doesnt/exist: No such file or directory [-Wmissing-include-dirs]
cc1plus: warning: bazel-out/k8-fastbuild/bin/external/bazel_tools: No such file or directory [-Wmissing-include-dirs]
Question 1: Where does bazel-out/k8-fastbuild/bin/external/bazel_tools come from and why is it missing?
Question 2: How do I write my bazel build so that this warning doesn't appear?
If I were to remove the inclusion of path/that/doesnt/exist from the cmake and bazel builds, and compile with flags -Wall -Werror -Wmissing-include-dirs, then the cmake build succeeds, but the bazel one fails.
Minimum working example found here: https://github.com/btk-learning/learn-to-build-cmake-bazel