In my belief, Splunk doesn't index the conf files. If you would like to index the conf files to track the change history on them, you can setup a monitor on different locations where .conf files can be present (etc/system, etc/apps, etc/users).
As far as I know there shouldn't be any issue monitoring .conf files.
Added to inputs.conf:
[monitor://C:\Program Files\Splunk\etc\...\*.conf] sourcetype = conf index = si_conf LINE_BREAKER=^\[ followTail = False
...*.conf looks at all subdirectories for any files with conf extensions.
^[ breaks events before each stanza
followTail was just added to get the entire file indexed each time. Haven't verified it yet.
I see the Configuration File Viewer, but I can't see the search that powers the stanza listing. Where is the information being indexed? ie: index=conf ... I am suspecting that it is not being indexed.
Confirming that the Configuration File Viewer uses btool to pull the data but does not index anything. We have to create searches with btools to send the data to summary indexes ourselves.