[CMake] Cleaning up some CMake warnings

In Bootstrap builds Clang logs some warnings. These are caused because Clang passes CLANG_STAGE and BOOTSTRAP_DEFAULT_PASSTHROUGH into the next stage's configuration.

BOOTSTRAP_DEFAULT_PASSTHROUGH shouldn't be passed, so it is renamed to _BOOTSTRAP_DEFAULT_PASSTHROUGH, to prevent passthrough.

CLANG_STAGE should be passed, so I've changed the code to log it if it is set outside the if(CLANG_ENABLE_BOOTSTRAP) block. This makes the variable always used, so the warning goes away.

llvm-svn: 276674