[compiler-rt] Reinstate removal of CRT choice flags from CMAKE_*_FLAGS* (#67935)

This reverts one part of commit
9f4dfcb7, with a modified comment added
about the code.

Ideally, this would only be reinstated temporarily - but given the
situation in vcpkg, it looks likely that they would keep passing the
duplicate options for quite some time. The conflicting CRT choice
usually are benign but only would cause warnings about one option
overriding the other, if passing e.g. "/MDd /MT".

However when vcpkg currently sets these options in CMAKE_*_FLAGS_DEBUG,
it passes the redundant option /D_DEBUG; thus the compiler finally ends
up with e.g. "/D_DEBUG /MDd /MT", which has the effect of defining
_DEBUG while using a release mode CRT, which allegedly breaks the build.

There's a PR up for removing this redundant /D_DEBUG option in vcpkg in
https://github.com/microsoft/vcpkg/pull/34123. With that in place, this
change wouldn't be strictly needed.