I made a similar observation to yours concerning -Wno-incompatible-pointer-types: If a source file didn't contain code that triggered warnings, then `cc1.exe: warning: unrecognized command line option "-Wno-incompatible-pointer-types"` wasn't printed by the toolchain.
Here is a more complete example of the occurrence of this warning:
C:\Users\Administrator\nta\nupic.core\build\scripts\ThirdParty\Source\Apr1StaticLib\misc\win32\apr_app.c:79:29: warning:
passing argument 3 of 'main' from incompatible pointer type
return main(argc, argv, env);
^
C:\Users\Administrator\nta\nupic.core\build\scripts\ThirdParty\Source\Apr1StaticLib\misc\win32\apr_app.c:48:12: note: ex
pected 'const char **' but argument is of type 'char **'
extern int main(int argc, const char **argv, const char **env);
^
C:\Users\Administrator\nta\nupic.core\build\scripts\ThirdParty\Source\Apr1StaticLib\misc\win32\apr_app.c: At top level: