Normally, this is the correct behavior. If your app is running under the virtual directory /app, then static files should be able to be requested using /app/content/site.css
. So your first focus should be on trying to understand why this is not working.
If you really want to change this logic, look at ProcessVirtualPath
in T4MVC.tt.hooks.t4. You can change the way the path is handled, and easily make it relative if you like. Make sure to rerun the T4MVC custom tool after changing this file.