No, it should work as long as you deploy the config to the right place. You have two options, deploy the config to the indexers or to the forwarders (depending if these are Universal, light or heavy forwarders...). The best option would be to have this deployed to the indexers.
In this kind of distributed environments I always deploy an app called globalconfig to the indexers with all the automatic field extractions/lookups that I need. Also make sure that this settings have the rights permissions in order to work 😉
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