It's the recommended way to set those, and is more portable
(automatically prepends -D for GCC/Clang and /D for MSVC).
We still use CPPFLAGS for some pre-processor flags which are not
defines.
This has already been fixed in Mono both master and 2019-06 (no other branch other than the skipped 2019-04 branch uses pthread_mutexattr_setprotocol).
Include paths are processed from left to right, so we use Prepend to
ensure that paths to bundled thirdparty files will have precedence over
system paths (e.g. `/usr/include` should have lowest priority).