That is the same warning that was in linux-2.4.0, and it especially applied in the era when kernel headers used by glibc were symlinks in /usr/src/linux/include that pointed to /usr/linclude/linux, or vice versa. In other words, unpacking a different kernel into /usr/src/linux would overwrite the headers glibc was built against. Being that our kernel headers are real files in the base-dev extension, we don't have anything installed into /usr/src/linux. It is most likely harmless to have, especially as we don't update kernel verisons without a toolchain update.
Lunar linux and Gentoo I believe still uses the symlink to point to the currently used kernel source probably due to their package manager cd-ing into /usr/src/linux to do the kernel build, but Arch, Debian, CRUX, and others do not. It is a relic from having the kernel headers present there. The "build" symlink in /lib/modules to the current source is used by modern distros, as well as /usr/src/linux-VERSION.
WIth the proper BUILD symlink in /lib/modlues/`uname -r`, the symlink is most likely not needed for any builds of modern module packages. So I would personally agree that avoiding the /usr/src/linux symlink is good practice.