I made a little progress on this so I thought I would share.
Application Templates have nothing to do with the Applications you already have configured in UEM. UEM has preconfigured templates for some apps and you can see which ones they are by creating a new config file and choose Use an Application Template. UEM includes template for for Office 2013 and specifically includes Visio and Project.
Having said that, you do not appear to be able to use the UEM profiler to profile any app that there is a template for. If I wanted to change setting in Visio for example.the only way I see to do that is to use the template, and add those settings on the predefined settings tab. I dont appear to be able to profile it and capture all the intial config settings that it does. Every time a new user runs the app, they will have to wait for it to configure itself. I dont see any way around this.
