https://answers.splunk.com/answers/3184/hostname-in-inputs-conf.html
By default, Splunk creates $SPLUNK_HOME/etc/system/local/inputs.conf on first time run. You're overwriting that by copying $SPLUNK_HOME/etc/system/default/inputs.conf to $SPLUNK_HOME/etc/system/local/inputs.conf. Now, this should work, but it doesn't. I filed a bug, SPL-108269 to track it, but will probably be a while before anyone gets to it given pretty valid workarounds available. This will affect any modular input you're using, not just Stream.
My suggestion to you is to put your configurations you want to monitor in your own app, or at a the very least, put them in $SPLUNK_HOME/etc/apps/search/local/inputs.conf and not change the default of having your hostname determined at First Time Run and written to $SPLUNK_HOME/etc/system/local/inputs.conf.
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