As a part of my build process I generate some files that should be included when creating a clickonce deployment.
Here is a blog post of someone telling you how to incl
So you want to include files which are generated by a build.
I think, although you said that it's not an option, that the only solution is to perform a manual deployment via Mage or MageUI. Only that way you're in control between the build and the deployment. Can't you create a batch file to deploy your application? You can execute the batch file in the Post-Build event.