Up until our latest release, we did not really have support for Enterprise provision and the fact that you saw it in the Publish menu, was because it was recognized in our system as AppStore provision. In the latest release, we've introduced support for Enterprise provision, for more information refer to the Create and Install Certificate and Provisioning Profile for In-House Distribution
With that feature coming to life, the Enterprise provision would be available in the Build dialog as noted in our release notes
and not in the Publish dialog. This is not written in stone and we welcome feedback, where you believe is the proper place for this provision.