Look into project settings->build phases, you can run a script before/after building your project. You can also create various XCode targets for different logo/appname. This is the most 'elegant' and only way for now.
I'm also building same App for different publishers with different logo/name. Apple DID provide some methods to build targets in command line in lower version of XCode, but it's not avaliable for newer version since XCode 4(it's been a long time, hope my memory is right).