I think we have a special filter to prevent deployment of user.config since it is usually different in dev than in production and we don't usually want to accidentally deploy the dev user.config file to production. Files should not have to be included in the project, it should deploy all files except for specific extensions like .cs that we don't want to deploy. Otherwise of it required project membership it would never deploy the files from other projects like mojoPortal.Features.UI or WebStore. Those files get copied below the Web folder during post build events and are included when publishing the mojoPortal.Web project (aka the Web folder) from VS even though they are not part of the mojoPortal.Wenb project.
So, you'll need to deploy user.config manually if you really intend to include it in a published package.
Hope that helps,