Configuring a build using the --with-extra-cxxflags option doesn't affect the build of hotspot, at least on Linux.

For example, on Linux, adding --with-extra-cxxflags='-Wno-cpp' will cause that warning option to to be included in gcc invocations for (some? all? I haven't explored that question) builds outside the hotspot tree, but it isn't included when compiling files in the hotspot tree.