I have just learned about the possibility to use OTHER_CODE_SIGN_FLAGS to specify the keychain which includes the cert needed for building and signing an app. But unfortunately
None of these really works unless you have the simplest of scripted builds going. Like @Tyler said, PackageApplication doesn't support specifying the keychain, and some versions of xcode will require there be no duplicate certificates across keychains when they check dependencies.
Don't waste your times, just call Apple and ask them to rename one of your certificates (they will actually rename your company --- by appending a suffix --- and you just have to regenerate your certificates and update your profiles).