I don't know anything about nant, specifically what types of ZIP files it produces. But MSDeploy should handle most ZIP files created by Windows Explorer, or other tools. If you use another tool to create your ZIP files, you'll have to manually add the manifest.xml/parameters.xml files at the root in order for MSDeploy to consume them. That is how the microsoft app gallery works -> third parties create their own ZIP files (for Wordpress, Drupal, etc) and add these files to get things working.
THe parameters.xml file defines how files should be transformed during the deployment. For example, altering web.config files as they are written to change the connection strings for DBs.
MSDeploy can be used for first time deployment. The App gallery scenario is just this. First time creation of web applications. (think of it as a radically simplified web application setup framework).