Hi,
You are correct, applications that have build-in templates cannot be profiled.
Be you don't need to, because the templates capture all the personalization already.
If you still want to change the template to capture more settings, you can use the UEM Management Console to 'expand' the template and see the content of the template.
If you just want to push application settings to the users for Visio, you can do this without the profiler:
1. Create a Config File in the UEM Management console using the Visio template
2. Login as a test user and start Visio and configure Visio as it should be for all your users.
3. Logoff the test user.
4. In the UEM Management Console go to the pre-defined settings tab for the Visio config file and click 'Add'
5. use the 'Install' button and browse to the UEM archive (.ZIP file) of the test user that contains the Visio settings.
Voila 
Kind regards, Pim.