Appdata is used for per user configuration and data stores, to achieve a degree of user isolation. The system profile is not a template, it is the profile directory for the system user account, which is the user running the root IIS process host instance (note w3wp processes are run under the identity associated with an app pool not the root IIS process, and are not run from within a service host process).
check out this example using PSEXEC to login as system. just as %appdata% resolves to the logged in users ~\AppData\ directory, so to does it work for the System account:
Copyright (C) 2009 Microsoft Corporation. All rights reserved.
PS C:\Windows\system32> psexec -s \\localhost cmd
PsExec v1.98 - Execute processes remotely
Copyright (C) 2001-2010 Mark Russinovich
Sysinternals - www.sysinternals.com
Microsoft Windows [Version 6.1.7601]
Copyright (c) 2009 Microsoft Corporation. All rights reserved.