It sounds like you are using the NaCl SDK. Creating native Pepper plugins is not really supported, strictly speaking. It's really only there to make debugging easier. My guess is the NaCl SDK team didn't get around to making it easy to build trusted/native plugins on MacOS, since Xcode can be tricky. I'm not sure.
We definitely build trusted Pepper plugins on MacOS X for Chromium. You can look at the .gyp and .gypi files in ppapi/ in the chromium source tree, and see what gyp generates.
But again, this isn't really supported, so you're mostly on your own. We don't have support for distributing a native/trusted Pepper plugin to Chrome on any platform; your better bet is to use NaCl or PNaCl.