After completing the webagent registration on IIS, you observed that web.config is not updated with any siteminder related configuration.
Steps performed.
1. Configured the siteminder webagent for new site.
2. Ran webagent registartion wizard and verified webagent.conf and smshost.conf updated.
3. Restarted the IIS.
4. Confirmed that web.config is not modified.
Policy server version :12.80.0700.2758
Webagent version:12.52.109.2614
The web agent configuration wizard will not update the web.config file of the IIS, the integration is done in %windir%\System32\inetsrv\config\applicationHost.config file.
In some cases, if you have legacy application which is still 32bit and requires to be running in legacy IIS mode, then some configuration changes will go into the site level to override the global level config. In those case, you can modify web.config file manually.