In pracitce, those root CAs have already been removed in major browsers. If your server uses them, you would likely have needed to migrate to another root already.
Apple’s own security framework is supported by curl with OpenSSL or GnuTLS (build with ./configure --with-apple-sectrust). That blocks the intermediate certificates via the same mechanism Safari uses for example.
Not sure why macOS doesn’t ship such a build of curl.
I think it’s possible to add intermediate certificates with distrust marker attributes to bundles with OpenSSL. But other libraries consuming the bundle would not understand it, so the problem remains.