transformations will apply to all incoming events. However, if you are only using a small subset of the app, you can only enable those data inputs from inputs.conf file. This way, transform.conf will only apply to the enabled data.
Just a reminder, only If the indexer is also a *nix host and you want to collect *nix data from it, should you enable the data and scripted inputs inside the Splunk_TA_nix add-on on the host. Otherwise, data collection should only happen on forwarders. Hope this helps.
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