Hi Ben,
The documentation that you found actually walks you through setting up the APM configuration which is different from an iApp. There are no iApps for Dynamics that come with the box in v10 or v11 (that I found, and found no results when I searched elsewhere).
The only mention I found of an iApp in the setup documentation revolves around the X-Forward-For header injection for your IIS Logging.
While the deployment guide is also the suggested and tested method...you can certainly use the deployment document for some portions of your setup and then use alternatives other than APM if you choose.
Sorry I couldn't be of more help.