The documentation on the site is out of date. In recent versions of MonoDevelop, these options are in your project settings under the item "Mac OS X Packaging". The app will now be packaged along with the build process, instead of having to do the extra step each time.
The default MonoMac project templates have an "App Store" build configuration that (by default) bundles the mono framework, signs the .app, and builds a .pkg that can be distributed to the app store.