For multiple targets, each task has to be done separately. And base the build (IPA) based on Xcode Schema File in xcode plugin.
And be sure to commit your code, set adhoc / appstore provisioning profile in your code signin according to your needs . After defining the provisioning profile for your desired env. commit your project.pbxproj.
And put your all provisioning profile under,
So, as your job running, it will automatically takes provisioning profile as per your Xcode Schema File name.